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Micro-organisms are very small life forms that are not visible to the naked eye. They include bacteria, viruses, fungi and microscopic parasites. Micro-organisms are found everywhere (on our bodies, in food, in soil, water and plants). Most micro-organisms are not harmful to humans and many actually colonise and protect us by preventing growth of pathogens.
Pathogens are micro-organisms that can cause disease (infection) and are potentially harmful to humans. To cause disease, these pathogenic micro-organisms must first be passed on (transmitted) to a person and then overcome the body’s defence systems.
Pathogens are micro-organisms that can cause disease (infection) and are potentially harmful to humans.
Micro-organisms are usually not visible to the naked eye:
Most bacteria are easily recognisable because they have particular shapes, staining characteristics and follow particular grouping or clustering patterns.
The shape of the bacteria varies for different families, for example they can appear round (cocci), rod-like (bacilli), spiral (spirochetes) or curved (vibrios).
Figure 2-1: Basic shapes and grouping patterns of bacteria
Bacteria can also be classified based on their staining pattern. The Gram stain is the most commonly used laboratory method to identify the staining pattern of bacteria. A smear is made on a glass slide of a fluid, either directly from a clinical sample (e.g. pus) or from a culture of growing bacteria (in liquid broth or on solid agar plates). The slide is allowed to dry and then stained with violet (blue) dye, decolourised and then stained with pink dye. Those bacteria that keep the blue dye stain are called Gram positive and those that lose the blue dye (decolour) will appear pink and are referred to as Gram negative. The staining of bacteria also allows identification by shape, such as round cocci or long bacilli, and grouping pattern.
|Gram stain||Shape||Grouping pattern||Examples|
|Bacilli||Random||Klebsiella, E. coli|
|Poorly or not staining||Spiral||None||Treponema|
The grouping pattern that the bacteria take up when seen under the microscope after staining, can also help to identify the bacterial species. For example some bacteria (staphylococci) are clustered together (appearing like a bunch of grapes) and others occur in chains (streptococci, enterococci). Most of the gram-negative rods (bacilli) have no particular grouping pattern.
Mycobacteria form a group of bacteria causing diseases like tuberculosis (Mycobacterium tuberculosis) and leprosy (Mycobacterium leprae). They have a thick waxy layer that prevents the Gram stains from penetrating. Therefore a different staining technique called the Ziehl-Neelsen (ZN) stain is used, which allows a red dye (carbol fuchsin) to enter and stain the mycobacterial cells. Acid and alcohol are then applied to the slide which removes colour from all other bacteria, but not the mycobacteria (which is why they are sometimes referred to as acid and alcohol fast).
In microbiology laboratories, bacteria are grown on agar plates (essentially a jelly containing all the nutrients that bacteria need to grow). The laboratory can use other appearances (bacterial growth characteristics) on these agar plates to further identify the species. For example, colonies of Staphylococcus aureus bacteria growing on an agar plate have a characteristic golden yellow colour.
Bacteria can also be classified by their growth requirements such as the need for oxygen or carbon dioxide. Bacteria can be classified as aerobic bacteria (oxygen dependent), anaerobic bacteria (can grow in the absence of oxygen) and facultative anaerobic bacteria (can grow in the presence or absence of oxygen).
Bacteria are single-cell organisms that have all the structures needed for their survival and replication. All bacteria are surrounded by a rigid outer cell wall, which gives them their shape (Gram-positive bacteria have thicker cell walls than Gram-negative bacteria). The cell wall allows some substances in and out of bacteria through tiny channels (porins). Some bacteria have projections from the cell wall called pili and flagella. Pili help with bacterial attachment to host cells, while flagella allow bacteria to move. A thin membrane called the cytoplasmic membrane runs inside the cell wall and holds together all the cell contents. Important cell contents include the bacterial genetic material (DNA) and ribosomes (which act as factories producing more genetic material).
Figure 2-2: The structure of bacteria
Bacteria will grow best when they are in an environment that provides the correct combination of nutrients, temperature and humidity. The time taken to multiply (replicate) depends on the environmental conditions and bacterial species, but can be as fast as every 20 minutes. The growth cycle can be divided into four phases:
Fungi are made up of many cells with a thick cell wall. Most fungi multiply by forming long string-like filaments (known as hyphae), some produce fungal spores (a type of resting form that fungi take up under unfavourable conditions) and others (yeasts) grow by budding. Fungi can be commonly found in the environment and can also cause a variety of diseases in humans. Candida is the most commonly encountered fungal infection in healthcare settings. Fungal infections can be superficial (affecting the skin and subcutaneous tissue) or deep (affecting organs) or systemic, (spreading throughout the body). Deep and systemic fungal infections usually occur in hosts with weakened immune systems.
Viruses can only survive within host (human, animal or plant) cells, usually cells of the immune system. Once inside the host cells, viruses are relatively protected from the host’s defence mechanisms and can use the host structures to replicate. The intracellular location of viruses makes it difficult to produce drugs that kill the virus without causing damage to the host cell.
Viruses are categorised both by their genetic make-up (single- or double-stranded, RNA or DNA) and their shape. The virus’ shape (icosahedral, helical and complex) is determined by its nucleocapsid structure, which is a combination of viral nucleic acid and capsid (the outer shell). In some viruses the nucleocapsid is covered by an outer membrane (known as an envelope), whereas others are ‘naked’ or non-enveloped. Viruses without an envelope are more difficult to destroy or remove by disinfection.
Figure 2-3: The structure of a virus
Parasites include the sub-groups protozoa and helminths. Protozoal parasites are divided into four main types, grouped by their form (structure) and how they move (motility).
These worms are spread mainly by ingestion (swallowing) of the eggs. Certain helminths can be spread by insects (so-called vector-borne helminths which can infect blood and/or human tissues), e.g. Loa loa (onchocerciasis) and Wuchereria bancrofti (elephantiasis). The sub-group of helminths, known as flukes, include the parasites that cause bilharzia (Schistosoma haematobium) and gastro-intestinal diseases (Schistosoma mansoni and japonicum).
There are five main routes by which micro-organisms can be spread (see table 2-2).
|Main transmission route||Types of transmission||Examples|
|Contact||Direct||Hands of healthcare workers|
|Indirect||Equipment, e.g. thermometers, bedpans|
|Sexual||Sexual transmission of HIV or syphilis|
|Respiratory||Droplet||Influenza, many other respiratory viruses|
|Airborne (aerosols)||Tuberculosis, measles, chickenpox|
|Ingestion||Water||Contaminated water, e.g. cholera|
|Food||Contaminated food, e.g. salmonella|
|Faecal matter (faeco-oral)||Hepatitis A|
|Inoculation||Injection, trauma, surgery, blood products||Needlestick injury transmitting HIV, hepatitis B or C|
|Insects / Vectors||Mosquitoes transmitting malaria|
|Transplacental||Mother-to-child infections||HIV, syphilis, rubella, etc|
There is physical contact, which can be direct or indirect, between the host and the person or surface carrying the micro-organism.
The host breathes in micro-organisms which have been exhaled by an infectious person, in the form of respiratory droplets or aerosols.
The host either eats or drinks food or water that is contaminated by the micro-organism or touches a surface or person contaminated with faeces containing the micro-organism and then transfers the micro-organism into their mouth.
Micro-organisms can be introduced to the body through trauma, injections, surgical procedures or through the bite of an insect or vector carrying the micro-organism.
Micro-organisms circulating in the mother’s blood can cross the placenta during pregnancy causing infection in the fetus.
Contact transmission is the MAIN route of infection transmission in healthcare facilities.
For infection to develop the following are needed:
The sequence of infection transmission is sometimes called the ‘chain of infection’. It is the step-wise manner in which a micro-organism can be transmitted to a susceptible host.
The following steps are required to spread an infectious agent or micro-organism (see figure 2-4):
A reservoir is the environment where the micro-organism is usually found, e.g. Staphylococcus aureus is commonly found in the nose; Mycobacterium tuberculosis (TB) is commonly found in the lungs.
For example TB bacilli are coughed up from the lungs (respiratory tract) into the air.
For example, TB remains suspended in the air as aerosols (tiny particles containing the TB bacilli).
For example, TB bacilli suspended in the air may be breathed into the lungs of a person in the same room as the TB patient.
Figure 2-4: The chain of infection
There are two main ways in which micro-organisms are acquired and can cause disease:
It is important to know how an infection was acquired in order to prevent its spread to other susceptible people (hosts).
Once a micro-organism has been acquired, it must compete with the host’s local flora and withstand any host defences. Pathogenic micro-organisms that become established and persist on, or in, the host, are said to have colonised the host. Colonisation does not always result in infection or invasive disease in the host, but can be a potential source for transmitting the micro-organisms to other susceptible hosts.
Colonisation does not always result in infection, but can potentially transmit micro-organisms to other susceptible hosts.
To progress from colonisation to infection, a micro-organism must invade or penetrate through the host tissues and defences. Micro-organisms have a selection of ‘virulence factors’ which are mechanisms developed to overcome the body’s defences. Some pathogens also have special attachment mechanisms that allow them to find and enter specific host cells that will allow for survival and multiplication of the micro-organism.
Pathogenic micro-organisms can cause disease symptoms and signs by the following mechanisms:
Sometimes the symptoms or signs of disease are caused by the host’s own immune response to infection that is trying to remove the pathogen from the body, e.g. fever or a runny nose from the common cold (rhinovirus).
Micro-organisms can be acquired (endogenously or exogenously), can become established (colonisation) and then may progress to infection (under favourable conditions) producing symptoms and signs of disease. The host has several ways of preventing micro-organism invasion in the first place or containing and/or destroying the micro-organisms once invasion has occurred. In hosts that have compromised natural defences or weakened immune systems (immune-compromise), progression from colonisation to infection is more likely. Immuno-competent hosts (with intact natural defences and immune systems), are able to overcome most minor invasions.
The host has three main defence mechanisms (see table 2-3), namely:
|Main defences||Specific types of defence mechanisms||Explanation of defence mechanism|
|Physical barriers||Intact skin||When skin is damaged it is easier for pathogens to invade, e.g. burn wounds, drips|
|Mucous membranes||Mucus can surround invading micro-organisms and prevent attachment|
|Respiratory tract||Larger pathogens can be trapped in mucus and expelled from the airways by movement of tiny hairs called cilia|
|Normal flora||Reduce the ability of pathogens to colonise and multiply by competing for space and nutrients|
|Innate immunity||Complement cascade||A set of proteins that activate a chain of events causing inflammation, bursting of foreign and infected cells and removal by macrophages|
|Neutrophils and macrophages||Blood cells and immune cells of the liver, lungs, lymph nodes that activate a process (phagolysis) to destroy invading micro-organisms|
|Adaptive immunity||Immunoglobulin A (IgA)||This antibody is secreted from cells lining the gut and respiratory tract allowing for pathogen removal by other cells of the immune system|
|T-lymphocytes (cellular response)||These cells have special receptors that recognise bits of pathogens as foreign and can bind to infected cells|
|B-lymphocytes (humoral response)||These cells produce antibodies (specific anti-pathogen proteins) that trigger the complement cascade|
Normal flora (sometimes called commensals) are micro-organisms that live on and in the human body (colonise) without causing infection. Normal flora are mostly bacteria, although fungi and protozoa are also included. The number of bacterial flora living on the body actually outnumber the total of all the cells in the human body! Normal flora are found on the skin, in the respiratory, gastrointestinal and genital tracts. However, normal flora micro-organisms can cause infections if:
Normal flora are micro-organisms that live on and in the human body without causing infection.
Normal flora reduce the ability of pathogenic micro-organisms to colonise and multiply in the host by competing for space and nutrients. They can also produce chemical compounds (bacteriocidins) which kill other bacteria or make it difficult for other bacteria to grow by making the environment more acidic (lowering the pH). Normal gut and vaginal flora play a major role in preventing colonisation by pathogens.
Normal flora protect the human host by reducing pathogens’ ability to colonise and multiply.
There are many factors that increase the risk of acquiring an infection in a healthcare setting (see table below).
Table 2-4 demonstrates in greater detail the many factors that increase the likelihood of HAI occurring.
|Major factor||Specific factors||Explanation|
|Administrative||Staff shortages||Leads to shortcuts being taken which compromise IPC practice standards|
|Overcrowding of clinical areas||Increased risk of infection transmission by greater pathogen load and patients lying closer together|
|Lack of written IPC policies and structures||No formal guidance or practice standards that healthcare workers can be held accountable to|
|Lack of formal IPC training for staff; Use of untrained patient attendants||Staff and patient attendants who have not had any IPC training may be at risk of infection or may spread infections in a facility by incorrect or risky practices|
|Inadequate equipment||Equipment will be shared by many patients, often without any form of cleaning or disinfection|
|Inadequate facilities; poor hospital or facility design||Lack of appropriate infrastructure (washbasins, cough rooms, isolation rooms) can lead to poor IPC practice that increases the risk of HAI|
|Poor communication of infection risk||If staff and visitors are not made aware of potential infection risks, they cannot take the necessary precautions to prevent spread of disease|
|Environmental||Antibiotic resistance||Most healthcare facilities harbour antibiotic-resistant organisms|
|Excessive use of disinfectants||Overuse of disinfectants can also contribute to the development of resistant organisms|
|Poor waste management||Can expose staff and visitors to infection and attract pests if not properly disposed of|
|Clinical||Overuse of antibiotics||Excessive use of antibiotics selects out the most resistant organisms which then become established|
|Poor levels of hand hygiene||Poor compliance with hand hygiene increases contact transmission of infections|
|Poor implementation of transmission-based precautions||Failure to institute and enforce transmission-based precautions contributes to spread of pathogens|
|Lack of personal protective equipment (PPE)||Stock-outs or shortages of essential protective equipment hampers healthcare workers' ability to adhere to standard and transmission-based precautions|
|Patient||Extremes of age||Neonates, infants and the elderly are particularly vulnerable|
|Immunocompromise||Certain diseases (HIV, immune-deficiencies) and medications (e.g. steroids and anti-cancer drugs) can weaken a person's immunity to infection|
|Broad-spectrum antibiotic use||Can destroy a person's normal flora that play an essential role in the body's infection defences|
|Multiple invasive procedures||Any procedure, e.g. catheters, drips, mechanical ventilation, break the body's natural barriers and increase susceptibility to infection|
|Trauma and surgical procedures||The skin barrier is broken, resulting in easier entry for pathogenic micro-organisms|
|Prolonged hospital stay||The longer duration of stay exposes a patient to more pathogens|
|Pathogen||Primary invasive pathogens||Some organisms are by nature very invasive, e.g. Staphylococcus aureus|
|Opportunistic pathogens||These are normal flora organisms that can act as a pathogen under circumstances where the body's defences are weakened for some reason|
|Bacterial invasion||Some bacteria invade more easily after a viral infection, e.g. pneumococcal pneumonia after an influenza illness|
|High infecting dose||An organism is more likely to cause an infection if the initial bacterial load (inoculum) is large|
The spectrum of HAI includes any infection that develops 48 hours or more after hospitalisation.
HAI include site-specific infections, e.g. bloodstream, surgical site, skin and soft tissue, urinary, respiratory and gastrointestinal tract infections. HAI can also occur related to medical devices (so-called device-associated infections), e.g. central-line associated bloodstream infections (CLABSI), ventilator-associated events (VAE) and catheter-associated urinary tract infections (CAUTI).
Types of healthcare-associated infections include site-specific infections and device-associated infections.
The type of healthcare-associated pathogens (and their antibiotic susceptibility profile) will vary for each healthcare facility and will change over time. New pathogens can be introduced to a facility (e.g. with outbreaks) and will become more difficult to remove the longer they remain in the environment or on colonised patients or staff. Some facilities use a laboratory surveillance system for HAI, based on designated ‘alert organisms’. In such cases, a facility decides, based on the burden of HAI, which infection-associated organisms to monitor for and to investigate clinically when they are isolated. Typical examples of alert organisms include: methicillin-resistant Staphylococcus aureus; Acinetobacter baumanni; and Pseudomonas aeruginosa.
The risk of transmitting infections in healthcare settings can be reduced by applying interventions and changing staff behaviour. IPC interventions to reduce the risk of micro-organism transmission include: standard precautions and transmission-based precautions.
Standard precautions (previously called universal precautions) reduce the chance of infection transmission from both known and unknown (unrecognised) sources of infection. These precautions should be applied to all patients in all circumstances, whether or not they are known to pose an infection risk. Examples of standard precautions are safe injection practices, proper hand hygiene and use of appropriate personal protective equipment when exposed to blood and body fluids.
Standard precautions should be applied to all patients in all circumstances, whether or not they are known to pose an infection risk.
Transmission-based precautions (TBP) are interventions put in place to reduce the chance of infection transmission for particular pathogens, e.g. airborne precautions for TB. Remember that TBP are always applied in addition to standard precautions. Bear in mind too that many pathogens have more than one route of transmission, e.g. varicella (chickenpox) will need both airborne and contact precautions enacted.
A good working relationship between IPC and microbiology departments can contribute to better awareness of infection risks and improved IPC practices. In many settings accessing laboratory results is difficult, either because the laboratory is located far away or has insufficient staff to interact directly with clinical services. In such settings, the role of the IPC practitioner is critical to guide clinicians on how to contain potentially transmissible infections and to assist with outbreak investigation. A close relationship with the laboratory will help to gain access to urgent results with implications for management of patients (e.g. where isolation and/or transmission-based precautions are required).
Laboratory workers are at risk of acquiring infection through exposure to blood, body fluids, splashes and aerosols. Planning of laboratory design, safety features, work-flow and specimen handling techniques is essential to reduce this risk. In addition, laboratory workers should be fully immunised.
When using a microbiology service, it is important to remember that the quality of the result obtained is often directly influenced by how well the sample is taken and transported to the laboratory. The following basic tips will improve the outcome of your test:
The quality of the microbiology result obtained is often directly influenced by how well the sample is taken and transported to the laboratory.
Decisions regarding antibiotic treatment should be made keeping in mind the clinical picture – microbiology results should be considered only as a guide to treatment. Antibiotics are usually started as a ‘best guess’ (empirical therapy) and then later modified depending on clinical response (improvement or deterioration) and taking into account laboratory findings.
Microbiology results are especially helpful in antibiotic stewardship, which aims to reduce excessive or inappropriate use of antibiotics. For example, where no organisms have been isolated (or a viral infection is proven) and the patient is improving, antibiotics may often be safely discontinued. If a pathogen is identified, the antibiotic choice can be targeted (matched) to the particular pathogen isolated.
Remember that microbiology results (especially where samples have not been properly obtained) may reflect contamination with skin flora or pathogenic organisms that are only colonising the site, but not causing the infection.
Communicable diseases are illnesses transmitted by a pathogenic micro-organism from an infected person, animal, or reservoir to a susceptible host. IPC teams deal with patients hospitalised with communicable (infectious) diseases, as well as managing IPC practices in the community. Education of community-based healthcare workers, patients and caregivers in IPC is important in preventing spread of communicable disease and containing outbreaks.
Three main routes of transmission are recognised:
Several general public health measures can be used to reduce the occurrence of communicable disease or to contain communicable disease in an outbreak situation:
A nine-month-old baby with a congenital heart defect is admitted to a paediatric ward in heart failure. He is placed in a cot next to a child recovering from adenovirus pneumonia. Four days later the baby with the heart defect develops breathing difficulty and requires admission to the intensive care unit. A tracheal aspirate isolates an adenovirus. Blood cultures show no growth.
Adenovirus is transmitted by the respiratory route (droplet infection). Respiratory droplets containing the virus can be inhaled or introduced to mucous membranes by direct or indirect contact (e.g. touching an adenovirus-contaminated surface and then placing fingers in the mouth).
Any person without previous immunity (antibodies) to adenovirus can become infected (including other patients, staff, parents and visitors).
The original patient who was known to be recovering from adenovirus pneumonia should have been isolated and placed under droplet precautions. The importance of hand hygiene should have been emphasised to the staff caring for these patients. Knowledge of duration of infectiousness of certain organisms is helpful.
A 25-year-old man who has recently returned from Zimbabwe presents to his local clinic with a short history of profuse, watery diarrhoea and severe dehydration. He lives in a shack with no access to running water or toilet facilities. He is referred to hospital for intravenous rehydration. Over the following week, several more adults and children from the same informal settlement present to the local clinic with watery diarrhoea and dehydration. Stool specimens confirm that the cause of this diarrhoeal outbreak is Vibrio cholera.
Vibrio cholera is transmitted by the faeco-oral route through direct or indirect contact with contaminated water or an infected person’s body fluids (stool or vomitus).
Contact precautions should be implemented, ideally in a single room with en suite toilet facilities. If there are many affected patients, those with diarrhoeal disease (suspected to be cholera) could be nursed together (cohorted) in one room. Ensure easy access to personal protective equipment (gloves, aprons) for staff caring for these patients. Make sure linen and waste from these patients are handled as potentially infectious.
A clean water source will have to be supplied (if the water is cholera-contaminated) or the community must be shown how to safely decontaminate water by boiling or chlorination. Community members with gastrointestinal symptoms should be sent to a healthcare facility for management. Education regarding the importance of hand hygiene and clean water sources should be provided in all local languages.
A 56-year-old woman is admitted to hospital with 60% burn wounds to her body from a shack fire. She requires admission to ICU for ventilation and has a central line and urinary catheter inserted.
Her burn wounds have become infected with Pseudomonas aeruginosa and Acinetobacter baumanni. She has had multiple courses of broad-spectrum antibiotics. The microbiology laboratory calls you to inform IPC that she has cultured a very antibiotic-resistant Klebsiella pneumoniae (a carbapenem-resistant Enterobacteriaceae) from her last urine sample.
You will need to collect additional clinical and laboratory information on this patient. Review the clinical notes and speak to the attending doctor to establish if the patient has any symptoms and signs of a urinary tract infection. Check the urinalysis report for the presence of white cells (leucocytes) in the urine.
No, the risk of transmitting this highly resistant organism is just as great if the patient is colonised. The Burns Unit staff should be educated as to the potential for transmitting this organism to other patients.
The patient should be placed under contact precautions, and should ideally be put in a single room with en suite toilet facilities. Ensure easy access to personal protective equipment (PPE) (gloves, aprons) for staff. Try to provide dedicated equipment for this patient (to avoid the chance of carrying across this resistant bacteria to other patients). The Burns Unit staff should be educated as to the potential for transmitting this organism to other patients and the importance of excellent hand hygiene practice.
A severely ill eight-year-old boy is admitted to your casualty with a one day history of fever, exhaustion and muscle aches. He is noted to have extensive bruising. The doctor on call thinks that meningococcal septicaemia is the likely diagnosis.
The boy should be managed in isolation (away from other patients and visitors). The doctors and nurses caring for him should use contact and droplet precautions, since meningococcus can be spread through both these routes.
According to national policy, this is a telephonically notifiable disease, which must be reported to the local health authority within 24 hours of presentation to hospital. The local health authority usually co-ordinates the investigation of community and household contacts, and provides antibiotic prophylaxis to close contacts.
After 24 hours of appropriate antibiotic therapy, the patient can be de-isolated. It is very important to know (or to know where to find out about) the duration of contagiousness (infection risk) for different pathogens. This allows you (as an IPC practitioner) to make informed decisions on how long to recommend isolation of infectious patients.
A 26-year-old lady undergoes an emergency Caesarean section. Five days later her surgical wound looks infected and a wound swab grows a methicillin-resistant Staphylococcus aureus (MRSA).
Since this is a site-specific infection (surgical site) caused by an ‘alert pathogen’ (MRSA), which developed more than 48 hours after admission, it is classified as a healthcare-associated infection.
The most likely route or mode of infection is contact transmission (through the hands of healthcare workers). An important risk factor favouring the pathogen’s entry is the disruption of skin by the surgical incision.
All healthcare workers caring for this patient should use contact precautions (gloves and aprons). If possible, the patient should be placed in single-room isolation. Strict compliance with hand hygiene protocols should be enforced.
A 25-year-old recently married lady attends an outpatient clinic complaining of lower abdominal pain and painful micturition (passing of urine). The treating doctor requests urinalysis and a urine sample for laboratory microscopy and culture. Clear instructions are given to the patient regarding the sterile collection of a urine sample (to avoid contamination from the skin around the urethra).
The quality of the microbiology results will depend on how well the sample is collected. The chance of contaminating the urine sample (with normal flora from the skin in the genital area) is high. If the sample becomes contaminated at collection, it may be difficult to distinguish between growth of contaminants (skin flora) or true pathogens.
In this case, the patient developed the infection at home, so it is classified as a community-acquired infection. E. coli is a common cause of urinary tract infections and is usually considered an endogenous infection (acquired from the host’s own collection of micro-organisms, known as flora).