MicrobiologyBytes: Infection & Immunity: Bacteria Updated: October 21, 2004 Search

Bacteria - Basics Facts

Aims and Objectives

  • To describe a bacterium and the basics of bacterial taxonomy.
  • To outline the range of infections caused by bacteria and their investigation.
After reading this document, you should:
  1. Be familiar with the names of common bacteria of medical importance.
  2. Be able to give the Gram stain reactions of common bacteria of medical importance and understand their significance.
  3. Be aware of the colonisation sites of and infections caused by common bacteria of medical importance.
  4. Be aware of the methods used for the diagnosis of bacterial infection.

What are bacteria?

Bacteria are a successful and ancient form of life, quite different from the eukaryotes (which includes the fungi, plants and animals). They are small cells, found in the environment as either individual cells or aggregated together as clumps, and their intracellular structure is far simpler than eukaryotes. Bacteria have a single circular DNA chromosome that is found within the cytoplasm of the cell as they do not have a nucleus. Indeed they lack any of the intracellular organelles so characteristic of eukaryotic cells, such that they do not have the golgi apparatus, endoplasmic reticulum, lysosomes nor mitochondria. However they are generally capable of `free-living' and therefore they possess all the biosynthetic machinery that is needed for this, including 70S ribosomes (as opposed to the larger 80S forms found in eukaryotes) distributed throughout the cytoplasm. The most complex region of the cell is often the cell surface. The cell wall / outer membrane is described below, but in addition some bacteria may secrete a polysaccharide capsule onto their outer surface, some may have flagella which they require for mobility and some may have external projections such as fimbriae and pili which are useful for adherence in their chosen habitat. Although bacteria are generally far simpler than eukaryotic cells, they are extremely efficient within their own little niche - and this may include the ability to cause human infections. Bacteria multiply by binary fission and there is no sexual interaction.

Gram stain appearances of medically important bacteria

As bacteria are so small, they need to be viewed under a microscope using special stains; the stain that is traditionally used for this is called the "Gram stain". In this process, purple dyes are poured over bacteria that have been spread out thinly on a microscope slide and the cell walls of the bacteria (made out of peptidoglycan) take up the colour. If a solvent is then applied to the slide, bacteria which have only got a cell wall still keep their purple colour, but bacteria which have got an extra cell membrane (made out of phospholipid) outside their cell wall quickly lose the purple stain and become colourless; in order to be able to see these bacteria under the microscope a second red stain is then used.

A table of the staining characteristics for some common bacteria of medical importance is given below. Note that for cocci, it is not just the shape and colour of the individual bacterial cells that is important, but the way that all these cells group together too. Put simply, round purple balls that look like bunches of grapes under the microscope (i.e. Gram-positive cocci in clusters!) suggests that the bacteria are staphylococci. Most of these bacteria are fairly flexible about the conditions they require for their growth - give them roughly the right temperature and a few simple nutrients and they are happy. A few of them are rather more fussy though and bacteria such as Clostridium and Bacteroides are examples of this; they are called anaerobes which means that they can only grow if there is absolutely no oxygen present.

Gram positive Gram negative
Cocci (= round) Staphylococcus (in clusters) Neisseria (in pairs)
Streptococcus (in chains) Moraxella (in pairs)
Bacilli (= rod-like) Listeria Enterobacteriaceae (coliforms)
Bacillus Escherichia coli
Corynebacterium Klebsiella
Campylobacter (spiral)
Helicobacter (spiral)
Clostridium (anaerobic) Bacteroides (anaerobic)

Why should you bother with all this? There are three reasons:

Exceptions to the rule: not all bacteria are shown up by the Gram stain, but there are only a couple of important exceptions for you to remember now!

How do you get information about bacteria in clinical practice?

A number of different samples can be sent to the diagnostic laboratory for microbiological analysis including fluids (such as blood, urine or cerebrospinal fluid [CSF]), pieces of tissue or swabs taken from infected lesions. For specimens such as CSF that would normally be sterile, microscopy can be very useful as the presence of any bacteria is always abnormal. However, for the great majority of specimens, the sample will have to be spread out onto culture plates to grow the bacteria, to see if there are any in the sample that might be the cause of the infection - this will generally take at least 24 hours. If there are any suspect bacteria there, they will probably need to be identified further and also checked out to ensure that they are not resistant to the effect of antibiotics - at least another 24 hours. In situations where it is not possible to grow bacteria, it may be possible to diagnose infection based upon a person's antibody responses - but this is not usually a rapid method either! So that in many cases, you must make initial decisions about antibiotic treatment based upon a sound knowledge of bacteriology - what is the most likely or most important bacterial cause of this infection and what is the most appropriate antibiotic for treatment? This will usually be backed up by laboratory investigation to confirm your diagnosis (or not!) and help you refine your future management of the patient. To practice clinical medicine effectively you must have a good knowledge of bacteriology, some idea about the service provided by diagnostic laboratories and the ability to interpret the reports that are issued.

In the table of Gram stains above, the bacteria were grouped together and listed by genus name (plural = genera). This is a name given to a collection of bacteria that share many fundamental, major, obvious characteristics. However, by examining bacteria more closely, perhaps by looking at some of their biochemical capabilities for example, it is possible to divide them up further into individual species. This is very often of great clinical significance. An example of how this works in clinical practice is given below. Also, at the end of this chapter there is a table with a list of common bacteria of medical importance, the sites at which they can normally be found and the sorts of infections that they cause when things go wrong. This is intended to be a ready reference as you go through the course and you are not intended to learn all the information straightaway, but hopefully, by the end of the course, you will have become familiar with much of this information.

Case history:

A 77 year old man is 4 days post-op following an aortic aneurysm repair when he is noticed to have a temperature (37.5°C axilla) and he looks pretty unwell. He is a smoker and always produces a little sputum, but this has not increased in volume or colour and his cough is no worse than normal; his chest sounds fine using a stethoscope. He does not have any difficulty or pain when passing urine and his urine does not look cloudy. However, his wound does look a bit inflamed - there is some mild erythema and the leakage of a small amount of serous fluid.
He is allergic to penicillins. What is the cause of his temperature and what would your management be?


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Case review:
Obviously not all pyrexias are caused by infections - he could, for example, have a deep vein thrombosis or have a reaction to a blood transfusion but, based upon the history above, perhaps the most likely cause for his temperature would be a wound infection. Three different samples were first sent to the laboratory to help get a diagnosis; a sputum sample; a swab from the wound; and 2 sets of blood cultures as he does appear to be systemically unwell. Clearly there will be some delay before these can provide the answers, but, now that the samples have been taken, he can be started on antibiotics aimed at the most likely bacterial causes of wound infection. Top of the list is probably the bacterium Staphylococcus aureus, with Streptococcus pyogenes coming second. The treatment of choice here would normally be the antibiotic flucloxacillin, but he is allergic to this group of drugs and therefore he is started on the second best choice, erythromycin. In the laboratory after 24 hours, there is no growth from the patients blood and there are only the normal mixture of respiratory tract colonising organisms from the patient's sputum sample, but the skin swab has produced a heavy growth of some bacteria that are Gram positive cocci in clusters under the microscope. This suggests that he has staphylococci in the wound, but by itself this is not much help because some staphylococci are just normal, harmless inhabitants of healthy skin (often called colonisers or commensals). Therefore these staphylococci were examined further in the laboratory by looking for the presence of a bacterial enzyme called coagulase that has the ability to clot human plasma. If they do not have this enzyme (coagulase-negative staphylococci), they are members of a species called Staphylococcus epidermidis and they can be ignored here - they do not cause wound infections. However, in this case they did have the coagulase enzyme (coagulase-positive staphylococci) and were therefore identified as the species Staphylococcus aureus, top of the list as the cause of his wound infection. The final step is to check and make sure that they are sensitive to the antibiotics. In this case these strains of Staphylococcus aureus turned out to be resistant to the action of erythromycin, but the antibiotic ciprofloxacin was found to be effective. So 48 hours after the samples were taken, the report was back on the ward. His temperature had not really settled on erythromycin and this report both explained that and suggested a more effective choice of antibiotic treatment to which he did respond.

This fairly simple case does illustrate a number of points:
The human body is not sterile - bacteria do not equal disease! Surfaces exposed to the external environment, such as the skin, vagina and upper respiratory tract, are teeming with bacteria, most of which are either harmless or positively beneficial. In terms of sheer numbers though, the digestive tract must hold the record - human faeces typically contains more than 10,000,000,000,000 bacteria/ml.

A clinical problem, such as a pyrexia, requires a provisional diagnosis before you can decide on the appropriate patient management. Infections of the respiratory tract, the urinary tract and the wound site are all common causes of a post-operative temperature, not to mention some of the non-infectious possibilities described above. Your initial decisions will probably be based upon clinical history and examination, but laboratory investigation is important as it allows you either to confirm your diagnosis or else modify your treatment when things are not going as smoothly as you had expected. A very large range of bacteriological investigations is available and you may not always know which are the most useful - the lab can help you there if you give them good clinical information. Microbiology takes time so that it is vital to get it right first time - what if the lab didn't know that this patient was allergic to penicillins and only tested flucloxacillin?

Clearly, if you want to get the best from the laboratory for your patients, good communication is desperately important.

Site of Infection and Colonisation by Some Medically Important Bacteria

Bacterium Colonisation site Site of infection / clinical syndrome
Bacillus anthracis none anthrax
Bacillus cereus (environment) food poisoning / food-borne enteritis
Bacteroides sp. large bowel abdominal sepsis, abscesses (including cerebral)
Bordetella pertussis none whooping cough
Campylobacter sp. none food-borne enteritis
Chlamydia pneumoniae none respiratory tract (atypical pneumonia)
Chlamydia trachomatis none genital tract, eye
Clostridium botulinum (environment) botulism
Clostridium difficile (large bowel?) antibiotic-associated diarrhoea (inc pseudomembranous colitis)
Clostridium perfringens large bowel (& soil) gas gangrene, abdominal sepsis, food poisoning
Clostridium tetani large bowel (& soil) tetanus
Corynebacterium diphtheriae (nasopharynx?) diphtheria
other Corynebacterium sp. skin / nasopharynx urinary tract, 'line' colonisation / infection
Enterococcus spp. (formerly Streptococcus) large bowel urinary tract, 'line' colonisation / infection, abdominal sepsis
Escherichia coli large bowel urinary tract, abdominal sepsis, neonatal septicaemia / meningitis
Haemophilus influenzae nasopharynx non-capsulate: respiratory tract (inc exacerbation COAD, middle ear)
  group b capsulate: epiglottitis, meningitis, osteomyelitis
Helicobacter pylori (stomach?) atrophic gastritis, peptic ulcer disease
Klebsiella sp. large bowel urinary tract, abdominal sepsis
Legionella pneumophila none Legionnaires disease (Pontiac fever, 'atypical' pneumonia)
Listeria monocytogenes (large bowel?) septicaemia / meningitis (esp neonates & immunosuppressed)
Moraxella catarrhalis nasopharynx respiratory tract (inc exacerbation COAD, middle ear)
Mycobacterium leprae none leprosy
Mycobacterium tuberculosis none tuberculosis
other Mycobacterium sp. (none?) rarely tuberculosis, possibly other infections in immunosuppressed
Mycoplasma pneumoniae none respiratory tract ('atypical' pneumonia)
Neisseria gonorrhoeae none gonnorhoea
Neisseria meningitidis nasopharynx septicaemia / meningitis
Proteus sp. large bowel urinary tract, abdominal sepsis
Pseudomonas aeruginosa large bowel urinary tract, abdominal sepsis, respiratory tract in cystic fibrosis patients
other Pseudomonas sp. large bowel 'line'; colonisation / infection
Salmonella typhi /paratyphi large bowel? typhoid fever
other Salmonella sp. large bowel? food-borne enteritis
Shigella sp. large bowel? food-borne enteritis
Staphylococcus aureus nasopharynx, skin skin & soft tissue (eg abscess / cellulitis / fascitis), food poisoning & other toxin-mediated disease, endocarditis, osteomyelitis
Staphylococcus epidermidis skin, nasopharynx 'line' colonisation / infection (& other prostheses)
Streptococcus agalactiae (Group B -haemolytic) vagina neonatal septicaemia / meningitis
Streptococcus pneumoniae nasopharynx respiratory tract (including lobar pneumonia, exacerbation COAD, middle ear), meningitis
Streptococcus pyogenes (Group A -haemolytic) nasopharynx skin & soft tissue (eg abscess / cellulitis / fascitis), pharyngitis (rheumatic fever, glomerulonephritis)
Streptococcus viridans skin / mouth / nasopharynx bacterial endocarditis
Vibrio cholerae none food-borne enteritis including cholera
COAD = Chronic Obstructive Airways Disease. Sp. = species.

NB: for some infections, e.g. with Salmonella , asymptomatic carriage of the organism may persist for some time, especially following infection. However, as this is generally only temporary it is not the same as true colonisation and has therefore been placed in brackets with a question mark in the above table.

© AJC 2007.