Biofilms and human infection – an introduction

Mr James W Fairley BSc MBBS FRCS MS
Consultant ENT Surgeon

Hadden Laureate in Microbiology, St Thomas’ Hospital Medical School, 1980

© 2007 – 2021 JW Fairley   Content last updated 18 August 2014


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Complexity of biofilm - opens link to source of image, Copyright Montana State University Center for Biofilm Engineering
Complexity of biofilm. © 2003 Center for Biofilm Engineering Montana State University-Bozeman

What is a biofilm?

A biofilm is a community of micro-organisms, attached to a wet or moist surface. Micro-organisms include

Individual micro-organisms can only be seen under a microscope. These bugs make a sticky, slimy, gel-like substance and surround themselves with it. It’s rather like frogspawn, but at a microscopic level. Some biofilms are a bit more solid. Biofilms are all around us in nature.

Two marvels of biological structural engineering. The skill that has gone into making this fine spider's web is clear.But there is an equally complex microstructure to the green film coating the inside of this glass outdoor lamp cover. It has built up on condensed water vapour. The complex structure of the biofilm can only be seen under high powered magnification.
Two marvels of biological structural engineering in niche environments. The skill that has gone into making this fine spider’s web is clear to the naked eye. But there is an equally complex, and more durable, microstructure to the slimy green film coating the inside of the glass outdoor lamp cover. It is no easy matter to hang on to a glass surface. The biofilm has built up on condensed water vapour. The complex structure of the biofilm can only be seen under high powered magnification.

Micro-organisms attach themselves to all kinds of surfaces. For example, a pebble in a pond is covered in slimy green stuff. That slime is a biofilm. The slippery layer that builds up inside a waste pipe is a biofilm.

Dental plaque is a biofilm containing many different species of bacteria, including some dangerous germs
The plaque that builds up between the gum and the tooth is a biofilm. This biofilm cannot be eliminated, but can be kept under control by proper dental hygiene. Lots of dangerous germs live in dental plaque. If they get into the bloodstream they can cause serious disease. Doctors and dentists knew this in the late 19th Century.

Biofilms also build up in humans. The one you will (or should) see every day is on the surface of your teeth.

Biofilms start as just a few bugs forming a thin layer. They can develop into complex, three dimensional structures housing millions of individual bugs. Like miniature cities, they have towers, columns, bridges and channels for the flow of nutrients. They are built by micro-organisms themselves, working together for their own protection.

Five stages of biofilm development Peg Dirckx and David Davies &copy 2003 Center for Biofilm Engineering Montana State University
Five stages of biofilm development.

  1. Initial reversible attachment of free swimming micro-organisms to surface
  2. Permanent chemical attachment, single layer, bugs begin making slime
  3. Early vertical development
  4. Multiple towers with channels between, maturing biofilm
  5. Mature biofilm with seeding / dispersal of more free swimming micro-organisms

Graphic by Peg Dirckx and David Davies &copy 2003 Center for Biofilm Engineering Montana State University.

A bug’s life

Bugs, germs, bacteria, micro-organisms – we think of them as dirty and dangerous, to be avoided, controlled, exterminated. But these are living creatures. They share a lot of DNA with us. They also share our needs for food, shelter and to keep their family line going – reproduction. Some bugs actually form partnerships with us. The friendly bacteria that live in our gut help us digest our food. Over millions of years of evolution, some micro-organisms became part of us. The relationship benefits both sides. Mitochondria are formerly free living bacteria that now live entirely within our own body cells. They  form the powerhouses of our muscles. We can’t do without them. Other bugs are passengers on the surface. They get a free ride, they do us no harm. But they can turn nasty. Good fences make good neighbours. If the skin is broken, bugs that have lived there peacefully for years turn into looters, opportunists, vultures. If their spread is not controlled, they can kill us. Once we are dead, they will decompose our bodies and return us as nutrients to the soil, where the rootlets of plant cells will thrive on us. We all carry with us the seeds of our own destruction. Or, from an ecological viewpoint, we are recyclable, and the bugs will do the recycling….

We know you’re in there

The germs we know and hate are those we can grow and see in the laboratory. The germ theory of disease is quite recent. Robert Koch formalised it in the 1880’s. Although ideas of contagion (passing disease from one person to another) are very old, and leper colonies and
were found in the ancient world, how diseases really spread was only discovered in the late 19th Century. Prior to that, it was thought that a miasma – foul smelling air – was the cause of disease spread.

St Thomas' Hospital, London, 1871 Architect H Currie based on Florence Nightingale's ideas of hygeine, sanitation, light, space and ventilation

St Thomas’ Hospital, London, 1871
Architect H Currie

Design based on Florence Nightingale’s ideas of hygiene, sanitation, light, space and ventilation

Florence Nightingale was a firm believer in the miasma theory. She banished “foul drains” from the newly designed airy, well ventilated wards of St Thomas’ Hospital in London in the 1870’s. Her School of Nursing stressed the importance of cleanliness, hygiene, clean air and fresh water. She was not impressed by the new germ theory of disease.

Meanwhile, Koch in Germany developed his postulates, which relied upon the ability to produce pure cultures of individual species of micro-organisms. Victorian doctors looked for specific bacterial causes for various diseases. They found them. Tuberculosis and cholera were two of the earliest. The overall benefit to humanity of these discoveries was enormous, and Koch certainly deserved his 1905 Nobel prize for medicine. But there was a downside. In the search for specific organisms, microbiologists neglected the fact that many infections are not due to a single, pure strain of a germ, but rather a number of different bugs taking advantage of niche environmental conditions in the body. The futile search for the single culprit continues to this day in routine clinical practice.

A tiny acorn is the same organism as the mighty oak
Conventional medical microbiology has spent the last hundred years studying acorns, while ignoring great forests of oak trees. Research is looking up, but most clinical laboratory microscopes remain focused on a very small part of the picture.
A tiny acorn is the same organism as the mighty oak

Why not take a swab and send it to the lab?

Culture means making germs grow in artificial conditions, in the laboratory. The common types of culture medium are plates of gel containing nutrients. Taking a swab, and plating it out, is a bit like sewing seeds. Some will germinate, and thrive. Others won’t. They prefer the living organism, and don’t grow under lab conditions. The type of organism that can be grown in culture is the free-swimming or planktonic form of the bug. We now know that these forms only account for a small percentage of the germs in the body. Most germs are not in the free-swimming form, yet almost all our conventional medical microbiology is based on the results of swabs and culture plates. With these methods, we see only a very limited part of the picture.

The same micro-organism can take several different forms during its life cycle. Conventional medical microbiologists have concentrated on one form only, the planktonic state. That’s like studying acorns at our feet, while ignoring the great oak tree above our head. Just like the caterpillar, which turns into a pupa before emerging as the butterfly, it’s all the same organism. If we look only with butterfly nets, we will find only butterflies. We will never discover the other stages in the life-cycle of the bug.

Not only that, but there are often several different bugs involved, especially in chronic diseases. Everyone likes a scapegoat. But blaming one individual bug is usually mistaken. Taking a swab from a chronic infection is like making arrests at the scene of a riot. Those who survive the journey to the police station will be identified. Bugs that grow from the swab were definitely there. Others may well have been there too. Some guilty parties may not have been picked up, some may not grow in the lab. When several different germs grow from one swab, deciding between culprits and innocent bystanders is a matter of judgement. That judgement is made on the basis of partial and biased evidence. The microbiology lab report needs to be taken with a very large pinch of salt. In most ENT infections, taking a swab for conventional microscopy, culture and sensitivity swab is of very limited value. The result can easily mislead doctors without specialist experience. As a prize-winning medical school microbiologist, I hardly ever take swabs.

A place to call my own

Tonsils removed - yellow spots are crypt debris
Tonsils removed – yellow spots are crypt debris

Crypt debris from the tonsils
Crypt debris from the tonsils is a biofilm, comprising dead layers of shed skin, trapped decomposing food, bacteria and other micro-organisms. This debris provides a sheltered home for germs. Antibiotics don’t penetrate into the crypt debris.

Biofilm in a tonsil crypt as seen under the microscope- links to full size image and article in Archives of Otolaryngology Head & Neck Surgery, 2003.
Biofilm in a tonsil crypt as seen under the microscope. Links to full size image and article in Archives of Otolaryngology Head & Neck Surgery, 2003.

Most bugs want somewhere to settle down and call home. A good home will have the basic necessities of life to hand. Different bugs need different things to thrive. Some need lots of oxygen, others prefer very little. Some like it hot. A few prefer cold. Most like it warm and wet. Especially the ones that like to live with us. Humid beings are a favoured billet. But first, they have to find a way of hanging on in there. They need some way of attaching themselves to our surfaces. Some make sticky glue, and also hide in deep dark holes. When you are microscopic in size, a hair follicle counts as a deep dark hole. So does a sweat gland, the gap between your tooth and the gum, and all kinds of nooks and crannies that you will see if you put the human body under a microscope. Tonsil crypts are a classic sheltered home for bugs.

A problem shared

By working together, bugs can do things they can’t achieve alone. If you are one bug trying to hang on to a slippery surface, you may or may not succeed. But if a whole bunch of bugs hold hands and do it together, the chances of holding on are improved. Some bugs specialize in holding on, then others use them as a foundation. A community of bugs builds up on top. Sometimes this is done in a cooperative, community spirited way. Other times the newcomers just take advantage, use and trample over and destroy the earlier settlers, maybe feeding on the remains. Communities are often made up of several different types of bug, each with their own specialist contribution to make.

Family and friends

Families of bugs and their friends are found together. Most bugs reproduce by individual cells dividing into two. The new pair then also divide, then the next generation, resulting in an exponential increase in numbers. Conditions have to be right for this to happen. Warm and wet is ideal for most bugs to reproduce. No sex is involved, there are no male and female forms of bacteria, but they can and do swap genetic material. Genes can be transferred both within and across species. One important type of genetic code that bacteria swap between them is antibiotic resistance.

Looking for somewhere to settle down

Bugs are always on the lookout for favourable spots to settle. The human body is one big potential camping site for germs. The body has to tolerate some degree of colonization, especially on surfaces. But there are limits. The surface layers of the body are, in the main, tough enough to keep bugs out. But if they are injured or weakened, there is an opportunity for bugs to invade deeper into the body. This will not normally be tolerated, because of the risk of unlimited spread. The invasion normally causes a reaction by the body’s immune system. Cells are mobilized to attack the invader, often with powerful chemical weapons. Human immune system cells can eat up and digest foreign micro-organisms. Bugs in a biofilm protect themselves against these attacks by grouping together and surrounding themselves with thick slime. Who can blame them? They are up against a huge organism with trillions of cells – us. Those bugs have formed a union. They are trying to even up the odds a little. Against our high-tech multi-cellular corporate biological war machine, designed to repel boarders, they need every trick in the book.

United we stand

From the bug’s point of view, being part of a big stable biofilm is a good place to be. It is much safer, compared with a single swimmer, alone in the hostile world. The bugs in the biofilm are like city dwellers. They live a settled, sheltered life, supported by family, friends and neighbours. But they do need to fulfill their mission, to go forth and multiply, to spread their genetic code.

To do this, the biofilm will send out scouts. Single swimmers, or sometimes small clumps, go looking for new pastures to colonize. These free swimming or planktonic forms are designed to find and settle on new ground, then rapidly reproduce. Nearly all conventional microbiology relies on detecting and culturing the free-swimming or scout form of the bacterium. Showers of bacteria are released. Like fish spawn, most will not survive. Those that do find fertile ground will need to establish themselves quickly, and set up new colonies. Because our microbiology laboratories are set up to find and deal with these rapidly replicating, colonizing bugs, and our antibiotic treatments are also directed against them, antibiotics do not work at all well on established biofilms. The bugs in the biofilm are not actively replicating, they are not forming new colonies, they take different forms altogether. The bugs in the biofilm form a reservoir, a sheltered, sleepy home base, which can hunker down and withstand an onslaught of antibiotics. The antibiotics don’t get rid of the biofilm because the bugs in the biofilm are not doing the things the antibiotics are designed to attack. Antibiotics will kill any free swimming forms, but once the antibiotic treatment has finished, more scouts can be sent out. Like guerilla warfare, terrorists with the support of an established community can go to ground and wait till the heat is off. They can then take a further opportunity at a later date.

Someone to talk to

Cells in a biofilm talk to each other using chemical signals to build microcolonies and to keep water channels open. Graphic by Bill Costerton and Peg Dirckx &copy 1997 Center for Biofilm Engineering Montana State University
Cells in a biofilm talk to each other using chemical signals to build microcolonies and to keep water channels open. Graphic by Bill Costerton and Peg Dirckx &copy 1997 Center for Biofilm Engineering Montana State University

Neighbours in the biofilm work together to build their niche environment.

  • Some bugs use their bodies to build support structures, arches, columns.
  • Others form the foundation and are good at sticking onto the host surface.
  • Some make the sticky goo or slime that protects them.
  • Others make sure water channels are kept clear, otherwise the cells in the middle won’t get their share of oxygen and nutrients.

To work together efficiently, the bugs need to talk to one another. They do so by chemical signals. These chemical signals offer a potential method of disrupting biofilms. If we can find a way of interfering with their signals, we may be able to stop biofilms from building up, or even make existing biofilms fall apart. This is a promising research area, with the potential for developing new treatments. But some of the chemical signals used by bacteria are also used by our own body cells. We aren’t so very different from the bugs, we all use snippets of the same genetic code. So we have to be careful we don’t harm the human cells. The trick will be to find signals that are important to the biofilm, but aren’t important to human cells, and disrupt those.

Is it infected, doctor?

Lots of patients ask me that question. Well, is it an infection? How do we know? Sometimes the answer is a straightforward Yes. A raging acute infection has classical signs of pain, redness, swelling of the part, and high temperature. Sometimes, the answer is a clear No, everything looks entirely normal. But often there is some low grade inflammation going on, nothing acute, subtle signs that not all is well. Some of these cases are probably due to biofilm formation. At present, our laboratory methods for detecting biofilm disease are not very good. In clinics, we rely on careful close-up inspection. For many years, ENT specialists have used high powered operating microscopes and endoscopes in clinic. These are currently the best available methods for diagnosing biofilm disease. This is likely to remain so until new and better laboratory methods are developed.

Cleanliness is next to godliness

Mrs Sylvia Fairley SRN graduate of the Nightingale School of Nursing. St Thomas' Hospital, London 1977 - 1984

Sylvia Fairley SRN
Nightingale School of Nursing
St Thomas’ Hospital London
1977 – 1984

the proper use of fresh air, light, warmth, cleanliness, quiet, and the proper choosing and giving of diet

Notes on Nursing, 1859
Florence Nightingale

You can keep bugs under control by physically removing them. They can be

  • scraped off
  • brushed off
  • washed off

Washing with plain water doesn’t always work. Some bugs have ways of hanging on in there. Soapy water is better. It makes your skin slippery, so bugs are more easily washed away. Some antiseptic soaps also kill germs on contact. Cleaning the skin with antiseptic soap and water is one of the best defences against spreading germs.

But some areas of the body can’t be cleaned easily, for example the skin of your ear canals. That is why the ear canal skin has a thin coating of wax, and a slow-moving conveyor belt system to move the dead layers of skin slowly from inside to out.

The linings of the nose, sinuses, and bronchi can’t be cleaned but have evolved the specialist self-cleaning mechanism of mucociliary clearance.

When these self-cleaning systems break down, the ground is right for the establishment of biofilms.

Biofilm diseases in ENT

Glue ear, certain chronic ear infections, some forms of sinusitis, and chronic tonsillitis are examples of probable biofilm disease in the ear, nose and throat.

Further reading – links

Biofilm basics – what is a biofilm – University of Montana Center for Biofilm Engineering

Definition of biofilm –

Medical and healthcare applications of biofilms – Montana State University Center for Biofilm Engineering

Biofilm, City of Microbes – Paula Watnick and Roberto Kolter, Harvard Medical School. © 2000 American Society for Microbiology

Footnote 2007: Biofilms – Focal sepsis rediscovered?

Recent interest in the clinical importance of biofilms bears striking resemblance to ideas of focal sepsis in the early 20th Century. Biofilms in humans are now thought to pose that same special danger of low grade organisms, which can remain latent for years, causing occult or cryptogenic focal sepsis.

Patrick Watson-Williams compared their activities with “insidious ravages of the death watch beetle… proceeding unnoticed for generations in the roof of our Westminster Hall”. He did not use the terrorist / guerilla warfare / safe base analogy, even though terrorist / guerilla tactics would have been known at that time, following the Boer war.


All information and advice on this website is of a general nature and may not apply to you. There is no substitute for an individual consultation. We recommend that you see your General Practitioner if you would like to be referred.