Microbiology for medical students and FY

Microbiology can be a daunting subject for medical students and junior doctors alike to approach. Confronted with masses of information and bacteria names more suited to winning scrabble competitions, it’s often difficult to know where to start! However, acquiring a good understanding of microbiology can be life-saving for your patients, so it is well worth doing!!!

Like all aspects of medicine, it is best to adopt a systematic approach to the issue. In the pages that follow, I have provided the basic framework that I still use to approach microbiological issues. Using this framework should help you better understand the likely aetiology of infections and the best treatment. Most hospitals also have antibiotic policies that apply a similar approach, and applying this framework will help you understand your local policy better. If in doubt when a Foundation doctor – it’s always best to ask either a senior or your local microbiologist!

• Millions of microorganisms (bacteria and fungi) can be found in the human body.

• Some of these microorganisms help in bodily function (such as digestion). Many others are neither helpful nor harmful.

• Microbiology is the study of these microscopic organisms and others not normally found in the human body, such as viruses and prions.

• In clinical practice, we are particularly interested in microorganisms that cause disease (a condition that impairs normal function and, as such, may cause illness).

• Microbiologists specialise in assisting with the diagnosis and treatment of infections caused by microorganisms.

• An INFECTION describes the invasion of body tissues by disease-causing microorganisms.

• Consider Bacteria – These are prokaryotic organisms (in other words, they lack a cell nucleus).

• A typical human has ten times as many bacterial cells in their body than human cells.

• Certain bacteria are usually pathogenic (i.e. cause disease), whilst others may possess the ability to become pathogenic in certain circumstances.

When confronted with a patient that you think may have an infection, ask the following 4 questions;

1. Where is the infection most likely to originate from?

2. What bacteria are present in that location and likely to cause that type of infection?

3. Which antibiotics best cover those bugs?

4. Are there any patient factors (e.g. allergies) to consider?

The following sections aim to help you answer these questions.

The first question to ask is where the likely source of the infection is; if that is, there is an infection present at all! This question can usually be answered by taking a detailed history, performing a focused examination and utilising simple investigations such as chest x/rays and urine dipsticks.

Examples of some common types of infection and clues;

• Cellulitis (redness/infection of the skin) – visible on examination.

• Pneumonia (inflammatory lung infection) – history of cough, crackles on chest, Chest x/ray changes).

• Meningitis (inflammation of the meninges) – history of fever, headache, neck stiffness. LP.

• Urinary tract infection – symptoms of pain passing urine, frequency. Urine dip.

Bacteria can be divided into two groups based on the characteristics of their cell wall. Gram-Positive bacteria stain blue on gram stain due to the presence of peptidoglycan in the cell wall. Gram-Negative organisms lack the outer peptidoglycan layer so don’t – they are counterstained pink.

In terms of which bacteria cause which infection, there are always exceptions but generally;

• Skin and soft tissue infections = Gram Positive organisms.Urinary tract infections = Gram-Negative

• Intra-abdominal infections = Gram-Negative

• Pneumonia = Mixed – Gram-Positive (pneumococci), Gram Negatives (Haemophilus, Moraxella) and atypicals.

• Meningitis = Mixed – Gram-Positive (pneumococci), Gram-Negative (Neisseria, Haemophilus).

As well as dividing bacteria up by their appearance on gram stain you can further subdivide them based on how they look under the microscope. The

The following table uses this classification to summarise the key bacteria that we commonly encounter in clinical practice; When to look out for these bacteria;

• Staphylococcus aureus – Can be found on the skin. Causes cellulitis, skin / soft tissue infection, endocarditis, discitis.

• Streptococci – A diverse group of bacteria found predominantly in the mouth / GI tract. Cause amongst other things tonsillitis, sinusitis, ear infections, pneumonia and meningitis. Watch out for Group A streptococci that can be particularly virulent!

• Clostridium difficile – Found in the bowel. Resistant to many antibiotics can cause an infection in its own right as a consequence of antibiotic use. A reminder of the importance of careful antibiotic prescribing!

• Listeria – Causes meningitis in neonates, the elderly and immunocompromised.

• Neisseria – Associated with 2 main infections; N. Meningitidis causes meningitis, and N. Gonorrhoea causes Gonorrhoea – see microbiology is not so complicated after all!

• Moraxella – May cause exacerbations of COPD.

• Salmonella and Campylobacter – commonest causes of food poisoning in the UK.

• E.coli – Common cause of urinary tract infection and intra-abdominal infections.

• Pseudomonas – Very resistant organism; resistant to many commonly used antibiotics. Commonly associated with hospital-acquired infections.

• Proteus – Associated with stones and recurrent urinary tract infections.

• Legionella – Spread by aerosols so that it may cause outbreaks. Can cause potentially life-threatening atypical pneumonia.

To find more information on these bacteria, sees other sections of this website.

Ideally, antibiotics should be guided by culture results, so it is always worth checking recent results. Sometimes, however, if a patient has an active infection and is unwell from this, it is necessary to start empirical antibiotics straight away while waiting for microbiological cultures to guide therapy further. In these cases, you can use the principles already discussed to guide your antibiotic choice. Though once again, it should be emphasised that different centres will have different preferences based on local sensitivity patterns, so always check with your local policy and, if in doubt, ASK.

I find it useful to crudely divide antibiotics into the following groups based on their spectrum of coverage as follows;

1. Super broad-spectrum antibiotics

2. Weaker broad-spectrum antibiotics

3. Gram-Positive specific antibiotics

4. Gram-Negative specific antibiotics

5. Anaerobic specific antibiotics

1. Super broad-spectrum antibiotics

E.g. Carbopenems (meropenem, Ertapenem, Imipenem), Piperacillin Tazobactam, Co-Amoxiclav, 2nd, 3rd, 4th generation cephalosporins (cefuroxime, ceftriaxone, cefotaxime, ceftazidime), Chloramphenicol, Tigecycline, Quinolones (ciprofloxacin, moxifloxacin) and Gentamicin.

Description – Industrial antibiotics. Cover most gram-positive, gram-negative and anaerobic infections (nb cephalosporins don’t cover anaerobes). Ideally reserved for very sick patients or those with very resistant organisms grown. These antibiotics are most associated with C.difficile infection. You need to remember they don’t cover everything (i.e. meropenem and tazocin don’t cover MRSA) and may not always get where they need to (i.e. tazocin will not penetrate the blood-brain barrier well as meropenem, for instance, to treat meningitis).

2. Weaker broad-spectrum antibiotics

E.g. Amoxicillin, Doxycycline, 1st generation cephalosporins (e.g. cefalexin), Trimethoprim, co-trimoxazole, nitrofurantoin.

Description – Workhorse antibiotics. Generally felt to be less associated with C.difficile infection. Less disruptive to normal flora than broader options. Cheaper. Still offer effective treatments for conditions like pneumonia (amoxicillin and doxycycline) and urinary tract infections (trimethoprim and nitrofurantoin) empirically and good step down options, for instance, to complete a treatment course after bacteraemia.

3. Gram-Positive specific antibiotics

E.g. Flucloxacillin, Glycopeptides (Vancomycin, Teicoplanin), Macrolides (clarithromycin, erythromycin), Clindamycin, Linezolid and Daptomycin.

Description – Specifically cover Gram-positive organisms very well. Flucloxacillin, for instance, is the best antibiotic to cover staph aureus (Offers better anti Staph aureus cover than tazocin, for example). With the exception of flucloxacillin (and most beta-lactams) usually will cover MRSA.

4. Gram-Negative specific antibiotics

E.g. Timentin, Azetreonam and Colistin.

Description – Specifically cover Gram-negative organisms. It can be useful if you know you are dealing with a gram-negative pathogen.

5. Anaerobic specific antibiotics

E.g. Metronidazole.

Description – Specifically cover anaerobic organisms. Many of the Super broad-spectrum antibiotics (E.g. carbapenems, piperacillin-tazobactam, co-amoxiclav, tigecycline and chloramphenicol) possess anaerobic cover too.

Before prescribing any antibiotic, always consider key patient factors, including;

• Any allergies?

• Any previous antibiotics they have had (tend to avoid repeated courses of the same antibiotic as you will select out for resistance).

• Any recent cultural results? History has a habit of repeating itself!

• Any contra-indications to using that antibiotic? E.g. You can’t use trimethoprim on anyone on methotrexate, and ciprofloxacin lowers seizure threshold, so it needs to be avoided in epilepsy (Always check the BNF or equivalent for contra-indications before prescribing).

• Age of the patient – The older the patient, the more likely they are to develop C.difficile diarrhoea, so we try to avoid certain antibiotics (such as ciprofloxacin, clindamycin and cefuroxime) most frequently associated with CDI in elderly patients.

Remember, antibiotics can save lives!

However, like any medicine – they can also do considerable harm, so always be careful when prescribing antibiotics.

Thanks!