{"id":461,"date":"2023-09-16T22:10:25","date_gmt":"2023-09-16T21:10:25","guid":{"rendered":"https:\/\/microregistrar.com\/?p=461"},"modified":"2023-09-16T22:10:34","modified_gmt":"2023-09-16T21:10:34","slug":"microbiology-for-medical-students-foundation-doctors","status":"publish","type":"post","link":"https:\/\/microregistrar.com\/?p=461","title":{"rendered":"Microbiology for medical students \/ Foundation Doctors"},"content":{"rendered":"\n

Introduction<\/em><\/strong><\/h2>\n\n\n\n

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\u2019s 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 \u2013 it\u2019s always best to ask either a senior or your local microbiologist!<\/p>\n\n\n\n

Background<\/em><\/strong><\/h2>\n\n\n\n

\u2013      Millions of microorganisms (bacteria and fungi) can be found in the human body.
\u2013      Some of these microorganisms help in bodily functions (such as digestion). Many others are neither helpful nor harmful.
\u2013      Microbiology is the study of these microscopic organisms and others not normally found in the human body, such as viruses and prions.
\u2013      In clinical practice, we are particularly interested in microorganisms that cause disease (a condition that impairs normal function and, as such, may cause illness).
\u2013       Microbiologists specialise in assisting with the diagnosis and treatment of infections caused by microorganisms.
\u2013       An INFECTION describes the invasion of body tissues by disease-causing microorganisms.
\u2013       Consider Bacteria \u2013 These are prokaryotic organisms (in other words, they lack a cell nucleus).
\u2013       A typical human has ten times as many bacterial cells in their body than human cells.
\u2013       Certain bacteria are usually pathogenic (i.e. cause disease), whilst others may possess the ability to become pathogenic in certain circumstances.<\/p>\n\n\n\n

A  Systematic approach to medical microbiology<\/em><\/strong><\/h2>\n\n\n\n

When confronted with a patient that you think may have an infection, ask the  following 4 questions;<\/p>\n\n\n\n

1.        Where is the infection most likely to originate from?<\/p>\n\n\n\n

2.        What bacteria are present in that location and likely to cause that type of infection?<\/p>\n\n\n\n

3.        Which antibiotics best cover those bugs?<\/p>\n\n\n\n

4.        Are there any patient factors (e.g. allergies) to consider?<\/p>\n\n\n\n

The following sections aim to help you answer these questions.<\/p>\n\n\n\n

Where is the infection?<\/em><\/strong><\/h2>\n\n\n\n

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.<\/p>\n\n\n\n

 Examples of some common types of infection and clues;<\/p>\n\n\n\n

\u2013       Cellulitis (redness\/infection of the skin) \u2013 visible on examination. 
\u2013       Pneumonia (inflammatory lung infection) \u2013 history of cough, crackles on chest, Chest x\/ray changes). 
\u2013       Meningitis (inflammation of the meninges) \u2013 history of fever, headache, neck stiffness. LP.
\u2013       Urinary tract infection \u2013 symptoms of pain passing urine, frequency. Urine dip.<\/p>\n\n\n\n

What type of bacteria causes infections in those locations?<\/em><\/strong><\/h2>\n\n\n\n

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\u2019t \u2013 they are counterstained pink.<\/p>\n\n\n\n

\nhttps:\/\/youtube.com\/watch?v=7Mok7d6BjNQ%3Ffeature%3Doembed\n<\/div><\/figure>\n\n\n\n

In terms of which bacteria cause which infection, there are always exceptions but  generally;
\u2013   Skin and soft tissue infections = Gram Positive organisms.
\u2013   Urinary tract infections = Gram-Negative 
\u2013   Intra-abdominal infections = Gram-Negative
\u2013   Pneumonia = Mixed \u2013 Gram-Positive (pneumococci), Gram Negatives (Haemophilus, Moraxella) and atypicals.
\u2013   Meningitis = Mixed \u2013 Gram-Positive (pneumococci), Gram-Negative (Neisseria, Haemophilus).<\/p>\n\n\n\n

Example of Gram-negative rods:<\/p>\n\n\n\n

\"\"
Gram negative rod (e.g. E coli)<\/figcaption><\/figure>\n\n\n\n

Bacteria  \u2013 Overview<\/em><\/strong><\/h2>\n\n\n\n

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;<\/p>\n\n\n\n

When to look out for these bacteria;<\/strong><\/p>\n\n\n\n

Staphylococcus aureus<\/u><\/em> \u2013 Can be found on the skin. Causes cellulitis, skin \/ soft tissue infection, endocarditis,  discitis.<\/p>\n\n\n\n

Streptococci<\/u> <\/em>\u2013 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 which can be particularly virulent!<\/p>\n\n\n\n

Clostridium<\/u> difficile<\/u><\/em> \u2013 Found in the bowel. Resistance to many antibiotics and can cause an infection in its own right as a consequence of antibiotic use. A reminder of the importance of careful antibiotic prescribing!<\/p>\n\n\n\n

Listeria<\/u><\/em> \u2013 Causes meningitis in neonates, the elderly and immunocompromised.

Neisseria<\/u><\/em> \u2013 Associated with 2 main infections; N. Meningitidis causes meningitis, and N. Gonorrhoea causes  Gonorrhoea \u2013 see microbiology is not so complicated after all! 

Moraxella<\/u><\/em> \u2013 May cause exacerbations of  COPD.<\/p>\n\n\n\n

Salmonella<\/u> and Campylobacter<\/u><\/em> \u2013  commonest causes of food poisoning in the UK.

E.coli<\/u><\/em> \u2013 Common cause of urinary tract infection and intra-abdominal infections.<\/p>\n\n\n\n

Pseudomonas<\/u><\/em>  \u2013 Very resistant organism; resistant to many commonly used antibiotics. Commonly associated with hospital-acquired infections.

Proteus<\/em> \u2013 Associated with stones and recurrent urinary tract infections.<\/p>\n\n\n\n

Legionella<\/u><\/em> \u2013 Spread by aerosols so that it may cause outbreaks. It can cause potentially life-threatening atypical pneumonia.<\/p>\n\n\n\n

To find more information on these bacteria, see other sections of this website.<\/p>\n\n\n\n

Which antibiotic should I choose?<\/em><\/strong><\/p>\n\n\n\n

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, it is necessary to start empirical antibiotics immediately 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.<\/p>\n\n\n\n

I find it useful to crudely divide  antibiotics into the following groups based on their spectrum of coverage as follows;<\/p>\n\n\n\n

1.        Super broad-spectrum antibiotics
2.        Weaker broad-spectrum antibiotics
3.       Gram-Positive specific antibiotics
4.       Gram-Negative specific antibiotics
5.       Anaerobic specific antibiotics<\/p>\n\n\n\n

Types of antibiotics<\/em><\/strong><\/h2>\n\n\n\n

1.       Super broad-spectrum antibiotics<\/strong><\/p>\n\n\n\n

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.<\/p>\n\n\n\n

Description \u2013 Industrial antibiotics. Cover most gram-positive, gram-negative and anaerobic infections (nb cephalosporins don\u2019t 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\u2019t cover everything (i.e. meropenem and tazocin don\u2019t 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<\/strong><\/p>\n\n\n\n

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

Description \u2013 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<\/strong><\/p>\n\n\n\n

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

Description \u2013 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.<\/p>\n\n\n\n

4.      Gram-Negative specific  antibiotics<\/strong><\/p>\n\n\n\n

E.g. Timentin, Azetreonam and Colistin.<\/p>\n\n\n\n

Description \u2013 Specifically cover Gram-negative organisms. It can be useful if you know you are dealing with a gram-negative pathogen.<\/p>\n\n\n\n

5.       Anaerobic specific antibiotics<\/strong><\/p>\n\n\n\n

E.g.  Metronidazole.<\/p>\n\n\n\n

Description \u2013 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.<\/p>\n\n\n\n

Patient  Factors<\/em><\/strong><\/h2>\n\n\n\n

Before prescribing any antibiotic, always consider key patient factors, including;<\/p>\n\n\n\n

a.       Any allergies?<\/p>\n\n\n\n

b.      Any previous antibiotics they have had (tend to avoid repeated courses of the same antibiotic as you will select out for resistance).<\/p>\n\n\n\n

c.       Any recent cultural results? History has a habit of repeating itself!<\/p>\n\n\n\n

d.      Any contra-indications to using that antibiotic? E.g. You can\u2019t 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).<\/p>\n\n\n\n

e.      Age of the patient \u2013 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 \u2013 they can also do considerable harm, so always be careful when prescribing antibiotics.<\/p>\n\n\n\n

Thanks<\/u><\/em><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

Introduction Microbiology can be a daunting subject for medical students and junior doctors alike to approach. Confronted with masses of […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ngg_post_thumbnail":0,"footnotes":""},"categories":[157],"tags":[],"class_list":["post-461","post","type-post","status-publish","format-standard","hentry","category-microbiology-for-medical-students"],"_links":{"self":[{"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/posts\/461","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/microregistrar.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=461"}],"version-history":[{"count":2,"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/posts\/461\/revisions"}],"predecessor-version":[{"id":640,"href":"https:\/\/microregistrar.com\/index.php?rest_route=\/wp\/v2\/posts\/461\/revisions\/640"}],"wp:attachment":[{"href":"https:\/\/microregistrar.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=461"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/microregistrar.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=461"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/microregistrar.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=461"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}