The identification of bacteria causes a lot of confusion and difficulty for students and doctors and having recently seen the microbiology lecture notes of a final year medical student, I’m not surprised. The notes talked about things
like “catalase positive DNAse positive, slide coagulase positive Gram-positive cocci” and “lactose-fermenting, indole positive, citrate negative, Gram-negative bacilli” which to anyone other than a microbiologist is just so much gibberish! (For the record, the first is Staphylococcus aureus and the second is E. coli).
like “catalase positive DNAse positive, slide coagulase positive Gram-positive cocci” and “lactose-fermenting, indole positive, citrate negative, Gram-negative bacilli” which to anyone other than a microbiologist is just so much gibberish! (For the record, the first is Staphylococcus aureus and the second is E. coli).
Why is microbiology made so complicated? This microbiology gibberish means nothing in the clinic or at the patient’s bedside and should be reserved for microbiology laboratories. It is however important that doctors can confidently identify common bacteria, and understand how this identification relates to clinical disease and their choice of antibiotics.
The first step in identification is the Gram film. This technique was developed in 1884 by a Danish scientist called Hans Christian Gram, and still forms the corner stone of bacterial identification today.
The Gram film will divide the bacteria into 3 broad groups; Gram-positive, Gram-negative and those that don’t stain at all. Both Gram-positive and Gram-negative groups can then be subdivided into cocci (round) and bacilli (elongated or rods), and then further divided as to their normal growth requirements (aerobic, anaerobic, facultative anaerobe or
microaerophilic). The group that don’t stain at all are either acid fast bacilli (like Mycobacteria) which have mycolic acid in their cell wall which does not allow the Gram’s stain in, or bacteria with a cell membrane but no cell wall so they do not retain the stain (see diagram below).
The first step in identification is the Gram film. This technique was developed in 1884 by a Danish scientist called Hans Christian Gram, and still forms the corner stone of bacterial identification today.
The Gram film will divide the bacteria into 3 broad groups; Gram-positive, Gram-negative and those that don’t stain at all. Both Gram-positive and Gram-negative groups can then be subdivided into cocci (round) and bacilli (elongated or rods), and then further divided as to their normal growth requirements (aerobic, anaerobic, facultative anaerobe or
microaerophilic). The group that don’t stain at all are either acid fast bacilli (like Mycobacteria) which have mycolic acid in their cell wall which does not allow the Gram’s stain in, or bacteria with a cell membrane but no cell wall so they do not retain the stain (see diagram below).
Click for a larger image
There are thousands of bacteria which can be identified however clinically only a handful are really relevant. Knowing, understanding and being able to identify these will be helpful on a daily basis to the junior doctor. Those really interested in bacteria can always learn an ever expanding list and become microbiologists!
At the end of the day confidently knowing a small list of the main clinical contenders in each group will serve most doctors most of the time when the lab calls and tells them a Gram film result from a specific tissue sample. The “must know” list:
Gram-positive cocci:
• Staphylococcus sp. (clumps)
• Streptococcus sp. (chains)
Gram-positive bacilli:
• Listeria monocytogenes (facultative anaerobe)
• Clostridium sp. (anaerobe)
Gram-negative cocci:
• Neisseria sp.
Gram-negative bacilli:
• Enterobacteriaceae e.g. E. coli, Klebsiella sp.,
Salmonella sp. (facultative anaerobe)
• Haemophilus sp. (facultative anaerobe)
• Pseudomonas sp. (aerobe)
• Bacteroides sp. (anaerobe)
The patient clinically has community acquired pneumonia; the lab rings with a Gram film result of the sputum showing Gram-positive cocci in clumps. Community acquired pneumonia is caused by Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenza, Legionella pneumophila, Mycoplasma pneumoniae and
Chlamydia sp. (see table below). As the result is Gram-positive this rules out Haemophilus influenza, which is Gram-negative and the Non-culturable bacteria: Legionella pneumophila, Mycoplasma pneumoniae and Chlamydia sp.
The microscopy also states clumps, which rules out Streptococcus pneumoniae, as this form chains. This leaves Staphylococcus aureus, a clump forming Gram-positive coccus.
At the end of the day confidently knowing a small list of the main clinical contenders in each group will serve most doctors most of the time when the lab calls and tells them a Gram film result from a specific tissue sample. The “must know” list:
Gram-positive cocci:
• Staphylococcus sp. (clumps)
• Streptococcus sp. (chains)
Gram-positive bacilli:
• Listeria monocytogenes (facultative anaerobe)
• Clostridium sp. (anaerobe)
Gram-negative cocci:
• Neisseria sp.
Gram-negative bacilli:
• Enterobacteriaceae e.g. E. coli, Klebsiella sp.,
Salmonella sp. (facultative anaerobe)
• Haemophilus sp. (facultative anaerobe)
• Pseudomonas sp. (aerobe)
• Bacteroides sp. (anaerobe)
The patient clinically has community acquired pneumonia; the lab rings with a Gram film result of the sputum showing Gram-positive cocci in clumps. Community acquired pneumonia is caused by Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenza, Legionella pneumophila, Mycoplasma pneumoniae and
Chlamydia sp. (see table below). As the result is Gram-positive this rules out Haemophilus influenza, which is Gram-negative and the Non-culturable bacteria: Legionella pneumophila, Mycoplasma pneumoniae and Chlamydia sp.
The microscopy also states clumps, which rules out Streptococcus pneumoniae, as this form chains. This leaves Staphylococcus aureus, a clump forming Gram-positive coccus.
Click for larger image
Having now refined the cause, Staphylococcus aureus, an antibiotic specifically targeted to that bacteria can be given. The patient is currently being treated with Amoxicillin by their GP as 90% of CAP is caused either by viruses or
Streptococcus pneumoniae (approx 24% and 65% respectively) but the patient is not improving because Staphylococcus aureus is not sensitive to Amoxicillin.
Staphylococcus aureus, although a cause of CAP, is only proportionally approximately 2%. Changing the treatment to Co-amoxiclav would be a better choice to target the causative organism (see table for spectrum of activity).
Streptococcus pneumoniae (approx 24% and 65% respectively) but the patient is not improving because Staphylococcus aureus is not sensitive to Amoxicillin.
Staphylococcus aureus, although a cause of CAP, is only proportionally approximately 2%. Changing the treatment to Co-amoxiclav would be a better choice to target the causative organism (see table for spectrum of activity).
Click for larger image
So bacterial identification is important, and Gram’s work from 1884 is still useful, but don’t get too bogged down in the detail, keep it simple and know the way to distinguish the common bacteria and choose an antibiotic specific to
those common organisms. Let a microbiologist deal with the catalase, coagulase and lactose-fermenting!
For more examples see Basic Bacterial Identification.
those common organisms. Let a microbiologist deal with the catalase, coagulase and lactose-fermenting!
For more examples see Basic Bacterial Identification.
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