The normal flora offers some protection against invading pathogens. The pattern resembles the problems 
of getting seeds to root in an established field of grain. The space is limited, the water and soil nutrients 
are all being taken by established root systems. This protection, when applied to the intestine, is called 
colonisation resistance, although the principle applies to any situation on the human body where the 
normal flora limits the ability of an invading organism to gain a foothold. The efficacy of this protection 
is highlighted by the disease pseudomembranous colitis(PMC). Patients with PMC develop severe 
diarrhoea and have a characteristic membrane over the surface of the colon visualised by 
sigmoidoscopy. PMC is caused by the multiplication and colonisation in the colon by the anaerobic 
Gram positive rod Clostridium difficile. When the normal intestinal flora is disrupted by treatment with 
poorly absorbed antibiotics, patients can become readily colonised by Clostridium difficile from sites 
vacated by the depleted normal flora. Clostridium difficile can produce at least two protein toxins that 
contribute to the diarrhoea that develops. The organism can be isolated from healthy people at low 
frequency, implying that the organism either exists in very low numbers in the gut and only multiplies 
when given the opportunity following antibiotic treatment, or is ingested at the appropriate time (in 
hospital, for example). 
Colonisation resistance applies to all sites where the normal flora is present. Within the vaginal tract, 
glycogen is present in relatively high concentrations due to the resident lactobacilli that produce lactic 
acid as the principle by-product of fermentation of glycogen. This production of acid lowers the pH to 
acid levels as low as pH 5, an environment that is antagonistic to many bacteria. 
Harbouring a normal flora is not without risks. Under normal circumstances the normal flora will most 
likely not present a problem. As soon as new and unusual circumstances arise, however, some microbes 
will seek to exploit a new potential site for growth and colonisation. Anyone who has cut themselves 
will recognise that often the cut becomes infected. Most likely it will be a Staphylococcus aureus
infection, the organism originating from the nose. Urinary tract infections by Escherichia coli will arise 
from the organisms that have passed through the gastrointestinal tract. Such organisms are thus termed 
‘opportunists’; they require a breakdown in the normal protective mechanism (e.g. cut in the skin). It is 

also possible to culture organisms that cause serious infections from a person who is asymptomatic. We 
can conclude thus far by saying that the relationship between host and the normal flora is in equilibrium 
until a perturbation of normal flora or host tissue occurs. Then the balance shifts in favour of the 
bacteria, rapidly multiplying in the new environment, at least in the short term. 
Knowledge of the dominant types of bacteria from the different sites of the body is essential when 

looking for pathogens in clinical samples. The use of appropriate selective culture media can be employed to help isolate any pathogens in a sample that may be 
dominated by normal flora (e.g. looking for salmonellae in faeces). The diagnostic microbiologist needs 
to learn how to recognise and distinguish the normal flora and the potential pathogen, not least because 
it is not always possible to obtain a specimen from the patient without sampling the normal flora as well 
as the diseased tissue. A patient with a chest infection needs to produce a sample by coughing. The 
difficulty is trying not to contaminate the sputum (from the lungs) with saliva and organisms from the 
normal flora of the mouth. These procedures are possible because the organism you are looking for is 
known and identifiable. Dental bacteriologists have not had it so easy. It is likely that tooth and gum 
decay is caused by the collective action of members of the normal mouth/gum flora. The problem arises 
because of the vast excess of glucose and other refined sugars that the modern diet provides. The marked 
acidity resulting from the fermentation of the sugar erodes the tooth enamel and enables a proliferation 
of anaerobic (hence, foul smelling) bacteria. It has been not been possible to convincingly identify a 
single culprit responsible for dental caries. 
You will have noticed that the normal flora has been contained to bacteria and yeasts that live on the 
external faces of the body (where the respiratory tract, genito-urinary tract, etc. are considered external 
faces). Internal organs are considered sterile. It is tacitly accepted that the presence of viruses is 
abnormal (i.e. an infection). The sequencing of the human genome has unearthed numerous stretches/
fragments of past virus infections. Whether viral genome in human tissues will ever be considered 
normal flora is up for debate. 
One important area of concern to hospital microbiologists is the problems of infections transmitted in 
hospitals. The topic brings together both the transmission of microbes and the state of the health in the 
host. Does illness cause a shift in the balance between the host and the microbes they encounter? 

Florence Nightingale said that going into hospital should at least do the patient no harm. Today, people 
often acquire an infection during their stay in hospital and these are called nosocomialinfections. The 
reasons are not hard to find. Patients will likely have one or more of their natural protective mechanisms 
breached. This can mean inserting an intravenous line or undergoing surgery, thereby breaching the 
intact skin barrier. Alternatively, if not in addition, they might have a urinary catheter inserted, thereby 
compromising the normal flushing by passing urine via the urethra. The opportunities for opportunistic 
microbes to establish an infection are provided. To further increase the risk, the patient will be visited by 
numerous staff and they themselves get the opportunity to touch and collect bacteria from all the other 
patients. Despite rigorous hand washing it is not always possible to remove all the bacteria. Nosocomial 
infections are opportunistic infections, considered separately from those infections acquired in the 
community. The distinction is usually made because the compromised condition of the patient leads 
them to be become infected with micro-organisms that, in healthy people, present little problem/risk. 

Not that hospitals are protected from ordinary infectious diseases. The infectious diseases that infect
healthy people outside of hospitals can easily be brought into hospitals via the staff. 
Infections that are acquired from external sources, i.e. are not normally resident within the host, are 
termed exogenousinfections. Those infections that originate from microbes present in the host normally 
are called endogenous. The terms ‘exogenous’ and ‘endogenous’ infection have particular value when 

investigating nosocomial infections because many infections arise from the patient’s own flora. If the infecting agent can 
be shown to be an exogenous infection it points to a problem of cross-infection. The term iatrogenic
infection applies to those infections that arise as a direct consequence of a medical or surgical procedure 
(e.g. infection of a new hip joint, infections following insertion of a urinary catheter or intravenous line). 
Iatrogenic infections, for example an infected intravenous line, can be either endogenous or exogenous 
in origin. The implications for control are obvious, the cost is another factor altogether. 
The sources of nosocomial infections are other people (staff or patients) or the patient’s environment. 
This will include such diverse sources as organisms growing in ventilator tubes, or inadequately 
disinfected endoscopes, through to organisms in the dust, air or food. In addition to the compromised 
defences of the patient, the bacteria that cause nosocomial infections are increasingly resistant to the 
action of antibiotics. Often, the organism is able to tolerate a range of different antibiotics (multiple 
antibiotic resistance), posing greater problems in the treatment of the infection. 
It is interesting that bacteria are the most common causes of nosocomial infections. However, more 
recent trends show an increasing incidence in fungal infections. It is suggested that the advances in 
medicine are paralleled by an increase in the number of infections by organisms of low virulence. The 
people who previously would have died, who now are being kept alive, are liable to acquire infections 
with organisms correspondingly ‘weak’. Whilst viral and fungal infections do occur, bacteria appear to 
be the dominant problem. Why? 
The reasons may be the source of nosocomial infections: humans and contaminated objects. Humans 
carry vast numbers of microbes as normal flora, and bacteria are able to quickly grow to large numbers 
in a wide variety of sites. Providing moisture and nutrients are available, bacterial growth will occur. 
Being microscopic, they will not necessarily be dealt with. Fungi may be able to grow on a wider range 
of substrates with less moisture (aw) but they form visible colonies of mycelia.The most frequent types of infection in hospitals occur in the urinary tract, bloodstream, the chest and in 
surgical wounds. The risk of developing a nosocomial infection is related, mostly, to the severity of the 
underlying disease. Patients who have impaired defences, whether they are inherited diseases of 
impaired immunity or secondary to other diseases or the treatment are all called ‘immunocompromised 
hosts’. The efficiency of treating the infection corresponds to the resolution of the original pathology. In 
addition to the primary disease predisposing a patient to nosocomial infections, the treatment itself can 
often have an effect. Drug treatment to immunosuppress patients following transplantation or treatment 
of cancer with cytotoxic drugs will impair the host immune response. Antibiotic treatment itself will 
disturb the normal flora (and therefore the colonisation resistance) and can select for bacteria that are 
resistant to that antibiotic. 
The interactions between populations defined at the start of the chapter tends to imply that they are 
stable in nature. More correctly, these states will continually be challenged by new circumstances which 
result in changes in the interactions. The dynamic nature of population interactions is highlighted by nosocomial infections where the condition of the host, the patient, is temporarily (we hope) altered. The 
medical and surgical improvements have created a greater variety of situations for microbial exploitation with tremendous financial costs. The challenge for medicine is to attempt to treat 
disease with as minimal disruption to the patient’s physiology and normal host flora as possible. 
From such pragmatic issues we conclude this chapter by revisiting the biology of the micro-organism 
and the reasons for parasitic infections in humans. What are the costs and benefits in choosing to infect 

Cited By Kamal Singh Khadka
Msc Microbiology, TU.
Assistant Professor In PBPC, PU, PNC, LA, NA.
Pokhara, Nepal.

www.rightdiagnosis.com › Diseases › Nosocomial infections


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