The mWater testing guide

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Low-cost Water Microbiology Tests

the mWater guide
by John Feighery, PhD

Microbial contamination is the most common reason that water systems fail to meet World Health Organization (WHO) guidelines; therefore, microbial testing is a logical first step in monitoring water quality. The detection of actual human pathogens in water is complex and requires advanced microbiology techniques. Instead, we look for fecal indicator bacteria that are commonly associated with the contamination of water supplies by untreated sewage. Although many fecal indicators have been proposed, we recommend E. coli because it is most closely associated with sewage and is preferred by the WHO.

In this guide, we discuss the most common methods used for field microbiology tests, the tests that we believe are most suitable and where to purchase supplies. We are constantly evaluating new test technologies and updating this guide. We have only included tests that we have direct experience using and that have accumulated some evidence documenting their validity for surface, ground (or drinking) water quality monitoring. If you would like to suggest new tests to be evaluated, please contact us.

Test methods

The standard sample size for water microbiology testing is 100 milliliters (mL), although some methods use smaller volumes if the number of bacteria is expected to be high. Water samples should always be collected in sterile containers or bags using aseptic technique.

Test methods can be summarized into four broad categories:

  • Presence/absence. This test provides a simple positive or negative result. Generally, a growth medium is added to a certain volume of water (usually 100 mL or 10 mL). The growth medium may also contain a compound that changes color when it is used by certain bacteria. This type of test is useful for detecting compliance with a particular guideline, such as the WHO requirement for no E. coli to be present in a 100 mL sample. When repeated over a period of time, the proportion of positive samples is often related to the contamination risk.
  • Most probable number. This method divides the sample into parts, which are then isolated from each other so that each part is like a separate presence/absence test. Originally, this was done using separate test tubes but now there are more convenient products that provide hard or soft plastic compartments that can be easily sealed off from each other. The number of compartments that are positive is used to lookup the result in a table. This result is called the Most Probable Number (MPN) because it is a statistical estimate that has an uncertainty range associated with it.
  • Direct count. In a direct count method, the actual number of bacteria are counted by isolating them from each other, providing a growth medium and then growing each bacteria into colonies containing billions of organisms that can be seen by the naked eye. The result is reported in colony-forming units (CFU) because we only know the number of colonies, which could have grown from a single bacterium or a clump of bacteria stuck together. Most direct count methods use a small sample volume of 1 mL or less because it must be spread across a plate to isolate the bacteria from each other, although some interesting approaches using gelling agents are now on the market for larger volumes.
  • Membrane filtration. In order to overcome the problem of small sample volumes usually associated with direct count methods, larger volumes of water samples can be filtered across a membrane that has pores that are too small for bacteria to pass through (usually 0.3 microns). The membrane is then aseptically transferred to a flat dish containing the culture medium, where the bacteria are grown.

For more information on selecting the right test and other tests, plus testing techniques and supplies, go to The mWater Guide at mWater!