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General Bacterial Overview


Bacteria are everywhere. We can’t function without them, but we often only hear about the bad guys.

What are they?

Bacteria, often referred to as "germs," are microscopic organisms that are present in water, soil and air, on and in animals, plants and man. They are bigger than viruses (which are only visible using an electron microscope), but smaller than molds (or fungi). They are able to multiply quickly, and need little in the way of "food." Since they are everywhere, all they really need to grow is water, just like molds. They are responsible for bad smells in the refrigerator and in damp basements (along with molds), evil smells in the bathroom (many of those smells are due to anaerobic bacteria: organisms that don’t like to grow in air), and some of them cause disease. The slimy film that coats your celery in the refrigerator is due to the growth of cold-resistant bacteria on the food, with the production of "biofilm."

What’s good about them?

  • Without them we’d be up to our necks in garbage. Bacteria and fungi break down dead things, and provide us with compost for the garden.
  • Even more seriously, we would not be able to digest our food. There are bacteria lining the digestive tract, which help us digest our food. The reason we get sicker with antibiotics is because they destroy the good bacteria as well as the bad. "Live" yogurt is spectacularly successful at treating tummy troubles or yeast infections following a course of antimicrobials because the yogurt replaces the bacteria we need. When good bacteria are removed, the "bad" guys take over, e.g., Candida, a type of yeast often responsible for those miserable yeast infections, is not killed by routine antibiotics, so it flourishes when the competing bacteria are removed.
  • Dead skin would be hanging off us without our friendly skin bacteria. Staphylococcus is often viewed as a bad guy, but this bacterium, along with Micrococcus and others, feeds on the dead skin cells and other debris. Those smelly anaerobes are also responsible for body odor, in all its gruesome forms, but they are an essential part of the food and garbage chain.
  • Without the microbes in general, we’d not have cheese, alcoholic drinks, yogurt, leavened bread or other fermented products. Life would be quite boring without these delicacies.

So what makes them bad?

It’s often when they are in the wrong place, like weeds (which are flowers or plants in the wrong place):
  • Staphylococcus works well on skin cells, but is horrid in wounds. The "wound" bench in the clinical microbiology laboratory was often called the "Staph. bench" because of the high amount of S.aureus found. It’s one of the bacteria responsible for impetigo, food poisoning, and toxic shock syndrome.
  1. The bacteria found in sewage are OK in the gut breaking down our food, but they’re disgusting when they back up into the kitchen sink along with the rest of the sewage. They smell bad, but they are also indicators, telling us that other, more dangerous organisms may be present, such as gastro-enteric bacteria and viruses.
  2. The operating room should not be a source of new infection for suffering patients. Why else would the surgeons dress up in those funny gowns, masks, hairnets and booties? They’re trying to avoid contaminating the patients with their germs/bacteria.
  3. It’s hopeless to pack sterile pills and potions in a room where there’s a lot of dirt and dirty air: sterile they’re not! That’s why pharmaceutical employees wear the same funny gowns, masks, hairnets and booties as surgeons. They are endeavoring to keep the "environmental load" down; in covering their hair, head, feet, mouth, etc. they are preventing their bacteria from being shed into the environment.
  4. Everyone has seen, heard, or, more particularly, smelled what happens to food that’s forgotten, either in the refrigerator, or, worse still, in a desk drawer.

If I can’t tell the good and bad guys apart, when should I test for bacteria?

  • Hospitals house sick patients. These people are very vulnerable to high levels of bacteria and mold. Hospitals need to know they are not infecting their patients, or allowing high numbers of organisms to be present in their environment. Patients with little or no immune systems (immunocompromised) can "catch" almost anything.
  • Pharmaceutical clean rooms need to be just that (see # 4 above).
  • Water we drink should be "clean." It should not contain sewage organisms at any level (see # 2 above). The sewage screen is a useful tool to show that our drinking water is good, or that the sewage leak was cleaned up properly.
  • Legionella is not a good thing in our hot water systems or in cooling towers: remember the Bellevue hotel in Philadelphia in the 70s? It was dead for some years because Legionnaires’ disease broke out in the hotel.
  • Because the client is concerned about bacteria in his/her environment.

How do I test for bacteria?

  • Provide us with a sample: water in a sterile container, a swab (we can supply these too), a bulk specimen in a clean plastic bag (e.g., soil, materials), air samples (collected on appropriate agar plates, using a high volume pump - see Sampling Guides at
  • Let us know what you are looking for, e.g., water is the preferred matrix for Legionella: it is an aquatic bacterium that will not be found on environmental Tryptic Soy agar plates (TSA). Water, swab and bulk specimens can be used for sewage screens. TSA plates are best for testing environmental loads. TSA with blood agar would be the medium of choice for potential pathogens.

AN IMPORTANT NOTE: You will not always find what you are looking for. Some pathogens are rarely found in the air: they are either too sensitive to its drying effects, or they are overgrown by competing environmental organisms. This does not mean they are not there, and is one of the reasons why "indicator organisms" are used for sewage screens. The gastro-enteric organisms, such as Campylobacter, Shigella, and even Salmonella, are almost never found in water, which is why we look for E.coli, fecal Strep., fecal and total coliforms in our sewage screens. Except for total coliforms, if any of these are present, then so is sewage, and by implication the Bad Guys. Presence of total coliforms only indicates dirt, but not sewage. Therefore it is important for you to contact the laboratory if you have questions about bacterial testing, or any type of microbiological testing.

What will the results look like?

    1. Sewage screens generally provide presence or absence of the indicator organisms (we can provide numbers for fecal coliforms and fecal Strep.).
  • Legionella testing will provide presence or absence of Legionella pneumophila in the submitted specimens.
  1. Bacterial count and gram stain will provide enumeration (in colony-forming units, or cfu, per mL, per gram, or per cubic meter of air, depending on the specimen submitted) and gram stain morphology of bacteria present.
  2. Identification of three (or five) predominant types will identify up to three (or five) predominant types of bacteria, predominance referring to the numbers present.

What do I do with the results?

There are no published standards or guidelines for bacteria in air. It is generally felt that a high level of gram negative rods in the air is unhealthy, especially of those bacteria associated with sewage. Presence of Legionella in water systems, fecal organisms in drinking water, or high levels of environmental organisms in a clean room or operating room are, however, not acceptable.
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