At the beginning of a recent medical student teaching session I was asked by a student why he should bother learning normal flora because what he really needed
to know was what causes infections. This is a particularly common and understandable approach from students but misses the significance of the most fundamental principle of microbiology or in fact medicine. If you do not know what is normal, how do you recognise abnormal? I smile inwardly and count to ten before going on to explain the importance of this often overlooked bit of knowledge.
to know was what causes infections. This is a particularly common and understandable approach from students but misses the significance of the most fundamental principle of microbiology or in fact medicine. If you do not know what is normal, how do you recognise abnormal? I smile inwardly and count to ten before going on to explain the importance of this often overlooked bit of knowledge.
Normal flora are the micro-organisms that live on another living organism (human or animal) or inanimate object without causing disease. The human body is not sterile; we become colonised by bacteria from the moment we are born. We are covered with, and contain within our intestines, approximately one hundred trillion bacteria that form the normal flora of our bodies. This normal flora helps to prevent us becoming colonised with more dangerous bacteria, which might lead to infection. Isolating micro-organisms from their normal body site is normal and does
not indicate infection.
not indicate infection.
Click for larger image
It is important to remember that 85-90% of infections are
derived from a person’s normal flora getting in to a site it should not be in. These are called endogenous infections. This is either from direct extension from a nearby site or by distant spread. By knowing the normal flora for a site and what antimicrobials these micro-organisms are normally sensitive to, allows you to predict the cause of an infection and derive an appropriate treatment regimen. For example, pneumonia tends to be caused by bacteria from the URT;
knowing what the normal flora of the URT is allows prediction of the antibiotics necessary to treat pneumonia. What’s more by understanding how antibiotics will impact on this normal flora (e.g. remove sensitive bacteria leaving a void which could be filled by resistant bacteria); you can determine what the likely cause of an infection will be, in a patient who has recently received antibiotic treatment.
Secondly, knowing where micro-organisms normally live allows you to work out where a pathological process is taking place when you find that micro-organism in a normally sterile site. For example, the presence of E. coli
(which normally lives in the bowel) in a blood culture indicates a significant problem in the abdomen either in the bowel itself such as in colitis, or in an adjacent structure such as the urinary tract or biliary tree. Another example,
isolation of a Viridans Streptococcus in blood cultures may indicate infective endocarditis as a result of poor dentition as Viridans Streptococcus are part of the normal mouth flora.
derived from a person’s normal flora getting in to a site it should not be in. These are called endogenous infections. This is either from direct extension from a nearby site or by distant spread. By knowing the normal flora for a site and what antimicrobials these micro-organisms are normally sensitive to, allows you to predict the cause of an infection and derive an appropriate treatment regimen. For example, pneumonia tends to be caused by bacteria from the URT;
knowing what the normal flora of the URT is allows prediction of the antibiotics necessary to treat pneumonia. What’s more by understanding how antibiotics will impact on this normal flora (e.g. remove sensitive bacteria leaving a void which could be filled by resistant bacteria); you can determine what the likely cause of an infection will be, in a patient who has recently received antibiotic treatment.
Secondly, knowing where micro-organisms normally live allows you to work out where a pathological process is taking place when you find that micro-organism in a normally sterile site. For example, the presence of E. coli
(which normally lives in the bowel) in a blood culture indicates a significant problem in the abdomen either in the bowel itself such as in colitis, or in an adjacent structure such as the urinary tract or biliary tree. Another example,
isolation of a Viridans Streptococcus in blood cultures may indicate infective endocarditis as a result of poor dentition as Viridans Streptococcus are part of the normal mouth flora.
Click for larger image
The presence of specific bowel bacteria in blood cultures can also be of diagnostic value as they signify malignant pathology. These bacteria include, Streptococcus gallolyticus (formerly known as S. bovis), Clostridium septicum and Streptococcus dysgalactiae (the Group G Beta-haemolytic Streptococcus). Providing a diagnosis of early bowel malignancy based on a blood culture and initiating a curative procedure to be carried out is very rewarding. However unfortunately I have also seen patients where investigations have not been initiated and malignancies have been missed until the patient presents several years later with inoperable metastatic malignancy.
It’s important that doctors adopt a questioning attitude and ask “why has my patient got this infection?” not just “what antibiotic am I going to treat my patient with?” Some people believe bacteria have no place in our environment but bacteria are part of the normal environment. Using the knowledge of where normal flora comes from gives you an advantage, allowing you to identify the likely cause of infection and help you to know where to investigate. This knowledge is known by microbiologists, that is why they seem to identify where the problem is without even seeing the patient!…Microbiologists are not better at discovering
infection just better at knowing where micro-organisms should and should not be and applying this knowledge.
It’s important that doctors adopt a questioning attitude and ask “why has my patient got this infection?” not just “what antibiotic am I going to treat my patient with?” Some people believe bacteria have no place in our environment but bacteria are part of the normal environment. Using the knowledge of where normal flora comes from gives you an advantage, allowing you to identify the likely cause of infection and help you to know where to investigate. This knowledge is known by microbiologists, that is why they seem to identify where the problem is without even seeing the patient!…Microbiologists are not better at discovering
infection just better at knowing where micro-organisms should and should not be and applying this knowledge.
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