Environmental Sampling or Measurement

This text addresses the basic principles and methods of sampling environmental surfaces and other environmental sources for microorganisms.

1. General Principles: Microbiologic Sampling of the Environment


Before 1970, U.S. hospitals conducted regularly scheduled culturing of the air and environmental surfaces (e.g., floors, walls, and table tops). By 1970, CDC and the American Hospital Association (AHA) were advocating the discontinuation of routine environmental culturing because rates of healthcare–associated infection had not been associated with levels of general microbial contamination of air or environmental surfaces, and because meaningful standards for permissible levels of microbial contamination of environmental surfaces or air did not exist. During 1970–1975, 25% of U.S. hospitals reduced the extent of such routine environmental culturing — a trend that has continued.


Random, undirected sampling (referred to as “routine” in previous guidelines) differs from the current practice of targeted sampling for defined purposes. Previous recommendations against routine sampling were not intended to discourage the use of sampling in which sample collection, culture, and interpretation are conducted in accordance with defined protocols. In this guideline, targeted microbiologic sampling connotes a monitoring process that includes:


a) a written, defined, multidisciplinary protocol for sample collection and culturing;

b) analysis and interpretation of results using scientifically determined or anticipatory baseline values for comparison; and

c) expected actions based on the results obtained.


Infection control, in conjunction with laboratorians, should assess the health-care facility’s capability to conduct sampling and determine when expert consultation and/or services are needed.


Microbiologic sampling of air, water, and inanimate surfaces (i.e., environmental sampling) is an expensive and time-consuming process that is complicated by many variables in protocol, analysis, and interpretation. It is therefore indicated for only four situations:

  • The first is to support an investigation of an outbreak of disease or infections when environmental reservoirs or fomites are implicated epidemiologically in disease transmission. It is important that such culturing be supported by epidemiologic data. Environmental sampling, as with all laboratory testing, should not be conducted if there is no plan for interpreting and acting on the results obtained. Linking microorganisms from environmental samples with clinical isolates by molecular epidemiology is crucial whenever it is possible to do so.
  • The second situation for which environmental sampling may be warranted is in research. Well-designed and controlled experimental methods and approaches can provide new information about the spread of health-care–associated diseases. A classic example is the study of environmental microbial contamination that compared health-care–associated infection rates in an old hospital and a new facility before and shortly after occupancy.
  • The third indication for sampling is to monitor a potentially hazardous environmental condition, confirm the presence of a hazardous chemical or biological agent, and validate the successful abatement of the hazard. This type of sampling can be used to: a) detect bioaerosols released from the operation of health-care equipment (e.g., an ultrasonic cleaner) and determine the success of repairs in containing the hazard, b) detect the release of an agent of bioterrorism in an indoor environmental setting and determine its successful removal or inactivation, and c) sample for industrial hygiene or safety purposes (e.g., monitoring a “sick building”).
  • The fourth indication is for quality assurance to evaluate the effects of a change in infection-control practice or to ensure that equipment or systems perform according to specifications and expected outcomes. Any sampling for quality-assurance purposes must follow sound sampling protocols and address confounding factors through the use of properly selected controls. Results from a single environmental sample are difficult to interpret in the absence of a frame of reference or perspective. Evaluations of a change in infection-control practice are based on the assumption that the effect will be measured over a finite period, usually of short duration. Conducting quality-assurance sampling on an extended basis, especially in the absence of an adverse outcome, is usually unjustified. A possible exception might be the use of air sampling during major construction periods to qualitatively detect breaks in environmental infection-control measures. In one study, which began as part of an investigation of an outbreak of health-care–associated aspergillosis, airborne concentrations of Aspergillus spores were measured in efforts to evaluate the effectiveness of sealing hospital doors and windows during a period of construction of a nearby building. Other examples of sampling for quality-assurance purposes may include commissioning newly constructed space in special care areas (i.e., ORs and units for immunosuppressed patients) or assessing a change in housekeeping practice. However, the only types of routine environmental microbiologic sampling recommended as part of a quality-assurance program are a) the biological monitoring of sterilization processes by using bacterial spores and b) the monthly culturing of water used in hemodialysis applications and for the final dialysate use dilution. Some experts also advocate periodic environmental sampling to evaluate the microbial/particulate quality for regular maintenance of the air handling system (e.g., filters) and to verify that the components of the system meet manufacturer’s specifications (A. Streifel, University of Minnesota, 2000). Certain equipment in health-care settings (e.g., biological safety cabinets) may also be monitored with air flow and particulate sampling to determine performance or as part of adherence to a certification program; results can then be compared with a predetermined standard of performance. These measurements, however, usually do not require microbiologic testing.

2. Air Sampling

Biological contaminants occur in the air as aerosols and may include bacteria, fungi, viruses, and pollens. Aerosols are characterized as solid or liquid particles suspended in air. Talking for 5 minutes and coughing each can produce 3,000 droplet nuclei; sneezing can generate approximately 40,000 droplets which then evaporate to particles in the size range of 0.5–12 µm. Particles in a biological aerosol usually vary in size from <1 µm to >50 µm. These particles may consist of a single, unattached organism or may occur in the form of clumps composed of a number of bacteria. Clumps can also include dust and dried organic or inorganic material. Vegetative forms of bacterial cells and viruses may be present in the air in a lesser number than bacterial spores or fungal spores. Factors that determine the survival of microorganisms within a bioaerosol include a) the suspending medium, b) temperature, c) relative humidity, d) oxygen sensitivity, and e) exposure to UV or electromagnetic radiation. Many vegetative cells will not survive for lengthy periods of time in the air unless the relative humidity and other factors are favorable for survival and the organism is enclosed within some protective cover (e.g., dried organic or inorganic matter). Pathogens that resist drying (e.g., Staphylococcus spp., Streptococcus spp., and fungal spores) can survive for long periods and can be carried considerable distances via air and still remain viable. They may also settle on surfaces and become airborne again as secondary aerosols during certain activities (e.g., sweeping and bed making). Microbiologic air sampling is used as needed to determine the numbers and types of microorganisms, or particulates, in indoor air. Air sampling for quality control is, however, problematic because of lack of uniform air-quality standards. Although airborne spores of Aspergillus spp. can pose a risk for neutropenic patients, the critical number (i.e., action level) of these spores above which outbreaks of aspergillosis would be expected to occur has not been defined. Health-care professionals considering the use of air sampling should keep in mind that the results represent indoor air quality at singular points in time, and these may be affected by a variety of factors, including:


a) indoor traffic,

b) visitors entering the facility,

c) temperature,

d) time of day or year,

e) relative humidity,

f) relative concentration of particles or organisms, and

g) the performance of the air-handling system components.


To be meaningful, air-sampling results must be compared with those obtained from other defined areas, conditions, or time periods.


Several preliminary concerns must be addressed when designing a microbiologic air sampling strategy. Because the amount of particulate material and bacteria retained in the respiratory system is largely dependent on the size of the inhaled particles, particle size should be determined when studying airborne microorganisms and their relation to respiratory infections. Particles >5 µm are efficiently trapped in the upper respiratory tract and are removed primarily by ciliary action. Particles <5 µm in diameter reach the lung, but the greatest retention in the alveoli is of particles 1–2 µm in diameter.

Preliminary concerns for conducting air sampling

• Consider the possible characteristics and conditions of the aerosol, including size range of particles, relative amount of inert material, concentration of microorganisms, and environmental factors.
• Determine the type of sampling instruments, sampling time, and duration of the sampling program.
• Determine the number of samples to be taken.
• Ensure that adequate equipment and supplies are available.
• Determine the method of assay that will ensure optimal recovery of microorganisms.
• Select a laboratory that will provide proper microbiologic support.
• Ensure that samples can be refrigerated if they cannot be assayed in the laboratory promptly.


Bacteria, fungi, and particulates in air can be identified and quantified with the same methods and equipment. The basic methods include a) impingement in liquids, b) impaction on solid surfaces, c) sedimentation, d) filtration, e) centrifugation, f) electrostatic precipitation, and g) thermal precipitation. Of these, impingement in liquids, impaction on solid surfaces, and sedimentation (on settle plates) have been used for various air-sampling purposes in health-care settings.

Several instruments are available for sampling airborne bacteria and fungi. Some of the samplers are self-contained units requiring only a power supply and the appropriate collecting medium, but most require additional auxiliary equipment (e.g., a vacuum pump and an airflow measuring device [i.e., a flowmeter or anemometer]). Sedimentation or depositional methods use settle plates and
therefore need no special instruments or equipment. Selection of an instrument for air sampling requires a clear understanding of the type of information desired and the particular determinations that must be made. Information may be needed regarding:


a) one particular organism or all organisms that may be present in the air,

b) the concentration of viable particles or of viable organisms,

c) the change in concentration with time, and d) the size distribution of the collected particles.


Before sampling begins, decisions should be made regarding whether the results are to be qualitative or quantitative. Comparing quantities of airborne microorganisms to those of outdoor air is also standard operating procedure. Infection-control professionals, hospital epidemiologists, industrial hygienists, and laboratory supervisors, as part of a multidisciplinary team, should discuss the potential need for microbial air sampling to determine if the capacity and expertise to conduct such sampling exists within the facility and when it is appropriate to enlist the services of an environmental microbiologist consultant.


Selecting an air sampling device


The following factors must be considered when choosing an air sampling instrument:

• Viability and type of the organism to be sampled
• Compatibility with the selected method of analysis
• Sensitivity of particles to sampling
• Assumed concentrations and particle size
• Whether airborne clumps must be broken (i.e., total viable organism count vs. particle count)
• Volume of air to be sampled and length of time sampler is to be continuously operated
• Background contamination
• Ambient conditions
• Sampler collection efficiency
• Effort and skill required to operate sampler
• Availability and cost of sampler, plus back-up samplers in case of equipment malfunction
• Availability of auxiliary equipment and utilities (e.g., vacuum pumps, electricity, and water)

Liquid impinger and solid impactor samplers are the most practical for sampling bacteria, particles, and fungal spores, because they can sample large volumes of air in relatively short periods of time. Solid impactor units are available as either “slit” or “sieve” designs. Slit impactors use a rotating disc as support for the collecting surface, which allows determinations of concentration over time. Sieve impactors commonly use stages with calibrated holes of different diameters. Some impactor-type samplers use centrifugal force to impact particles onto agar surfaces. The interior of either device must be made sterile to avoid inadvertent contamination from the sampler. Results obtained from either sampling device can be expressed as organisms or particles per unit volume of air (CFU/m3).

Sampling for bacteria requires special attention, because bacteria may be present as individual organisms, as clumps, or mixed with or adhering to dust or covered with a protective coating of dried organic or inorganic substances. Reports of bacterial concentrations determined by air sampling therefore must indicate whether the results represent individual organisms or particles bearing multiple cells. Certain types of samplers (e.g., liquid impingers) will completely or partially disintegrate clumps and large particles; the sampling result will therefore reflect the total number of individual organisms present in the air.

The task of sizing a bioaerosol is simplified through the use of sieves or slit impactors because these samplers will separate the particles and microorganisms into size ranges as the sample is collected. These samplers must, however, be calibrated first by sampling aerosols under similar use conditions.

The use of settle plates (i.e., the sedimentation or depositional method) is not recommended when sampling air for fungal spores, because single spores can remain suspended in air indefinitely. Settle plates have been used mainly to sample for particulates and bacteria either in research studies or during epidemiologic investigations. Results of sedimentation sampling are typically expressed as numbers of viable particles or viable bacteria per unit area per the duration of sampling time (i.e., CFU/area/time); this method can not quantify the volume of air sampled. Because the survival of microorganisms during air sampling is inversely proportional to the velocity at which the air is taken into the sampler, one advantage of using a settle plate is its reliance on gravity to bring organisms and particles into contact with its surface, thus enhancing the potential for optimal survival of collected organisms. This process, however, takes several hours to complete and may be impractical for some situations.

Air samplers are designed to meet differing measurement requirements. Some samplers are better suited for one form of measurement than others. No one type of sampler and assay procedure can be used to collect and enumerate 100% of airborne organisms. The sampler and/or sampling method chosen should, however, have an adequate sampling rate to collect a sufficient number of particles in a reasonable time period so that a representative sample of air is obtained for biological analysis. Newer analytical techniques for assaying air samples include PCR methods and enzyme-linked immunosorbent assays (ELISAs).


3. Water Sampling


A detailed discussion of the principles and practices of water sampling has been published. Water sampling in health-care settings is used detect waterborne pathogens of clinical significance or to determine the quality of finished water in a facility’s distribution system. Routine testing of the water in a health-care facility is usually not indicated, but sampling in support of outbreak investigations can help determine appropriate infection-control measures. Water-quality assessments in dialysis settings have been discussed in this guideline.

Health-care facilities that conduct water sampling should have their samples assayed in a laboratory that uses established methods and quality-assurance protocols. Water specimens are not “static specimens” at ambient temperature; potential changes in both numbers and types of microbial populations can occur during transport. Consequently, water samples should be sent to the testing laboratory cold (i.e., at approximately 39.2°F [4°C]) and testing should be done as soon as practical after collection (preferably within 24 hours).


Because most water sampling in health-care facilities involves the testing of finished water from the facility’s distribution system, a reducing agent (i.e., sodium thiosulfate [Na2S2O3]) needs to be added to neutralize residual chlorine or other halogen in the collected sample. If the water contains elevated levels of heavy metals, then a chelating agent should be added to the specimen. The minimum volume of water to be collected should be sufficient to complete any and all assays indicated; 100 mL is considered a suitable minimum volume. Sterile collection equipment should always be used.


Sampling from a tap requires flushing of the water line before sample collection. If the tap is a mixing faucet, attachments (e.g., screens and aerators) must be removed, and hot and then cold water must be run through the tap before collecting the sample. If the cleanliness of the tap is questionable, disinfection with 500–600 ppm sodium hypochlorite (1:100 v/v dilution of chlorine bleach) and flushing the tap should precede sample collection.

Microorganisms in finished or treated water often are physically damaged (“stressed”) to the point that growth is limited when assayed under standard conditions. Such situations lead to false-negative readings and misleading assessments of water quality. Appropriate neutralization of halogens and chelation of heavy metals are crucial to the recovery of these organisms. The choice of recovery media and incubation conditions will also affect the assay. Incubation temperatures should be closer to the ambient temperature of the water rather than at 98.6°F (37°C), and recovery media should be formulated to provide appropriate concentrations of nutrients to support organisms exhibiting less than rigorous growth. High-nutrient content media (e.g., blood agar and tryptic soy agar [TSA]) may actually inhibit the growth of these damaged organisms. Reduced nutrient media (e.g., diluted peptone and R2A) are preferable for recovery of these organisms.

Use of aerobic, heterotrophic plate counts allows both a qualitative and quantitative measurement for water quality. If bacterial counts in water are expected to be high in number (e.g., during waterborne outbreak investigations), assaying small quantities using pour plates or spread plates is appropriate.945 Membrane filtration is used when low-count specimens are expected and larger sampling volumes are required (>100 mL). The sample is filtered through the membrane, and the filter is applied directly face-up onto the surface of the agar plate and incubated.

Unlike the testing of potable water supplies for coliforms (which uses standardized test and specimen collection parameters and conditions), water sampling to support epidemiologic investigations of disease outbreaks may be subjected to modifications dictated by the circumstances present in the facility. Assay methods for waterborne pathogens may also not be standardized. Therefore, control or comparison samples should be included in the experimental design. Any departure from a standard method should be fully documented and should be considered when interpreting results and developing strategies. Assay methods specific for clinically significant waterborne pathogens (e.g., Legionella spp., Aeromonas spp, Pseudomonas spp., and Acinetobacter spp.) are more complicated and costly compared with both methods used to detect coliforms and other standard indicators of water quality.


4. Environmental Surface Sampling

Routine environmental-surface sampling (e.g., surveillance cultures) in health-care settings is neither cost-effective nor warranted. When indicated, surface sampling should be conducted with multidisciplinary approval in adherence to carefully considered plans of action and policy.


Undertaking environmental-surface sampling


The following factors should be considered before engaging in environmental-surface sampling:


• Background information from the literature and present activities (i.e., preliminary results from an epidemiologic investigation)
• Location of surfaces to be sampled
• Method of sample collection and the appropriate equipment for this task
• Number of replicate samples needed and which control or comparison samples are required
• Parameters of the sample assay method and whether the sampling will be qualitative,
quantitative, or both
• An estimate of the maximum allowable microbial numbers or types on the surface(s) sampled (refer to the Spaulding classification for devices and surfaces)
• Some anticipation of a corrective action plan

Surface sampling is used currently for research, as part of an epidemiologic investigation, or as part of a comprehensive approach for specific quality assurance purposes. As a research tool, surface sampling has been used to determine:


a) potential environmental reservoirs of pathogens,

b) survival of microorganisms on surfaces, and

c) the sources of the environmental contamination.


Some or all of these approaches can also be used during outbreak investigations. Discussion of surface sampling of medical devices and instruments is beyond the scope of this document and is deferred to future guidelines on sterilization and disinfection issues.

Meaningful results depend on the selection of appropriate sampling and assay techniques. The media, reagents, and equipment required for surface sampling are available from any well-equipped microbiology laboratory and laboratory supplier. For quantitative assessment of surface organisms, non-selective, nutrient-rich agar media and broth (e.g., TSA and brain-heart infusion broth [BHI] with or without 5% sheep or rabbit blood supplement) are used for the recovery of aerobic bacteria. Broth media are used with membrane-filtration techniques. Further sample work-up may require the use of selective media for the isolation and enumeration of specific groups of microorganisms. Examples of selective media are MacConkey agar (MAC [selects for gram-negative bacteria]), Cetrimide agar (selects for Pseudomonas aeruginosa), or Sabouraud dextrose- and malt extract agars and broths (select for fungi). Qualitative determinations of organisms from surfaces require only the use of selective or non-selective broth media.

Effective sampling of surfaces requires moisture, either already present on the surface to be sampled or via moistened swabs, sponges, wipes, agar surfaces, or membrane filters. Dilution fluids and rinse fluids include various buffers or general purpose broth media. If disinfectant residuals are expected on surfaces being sampled, specific neutralizer chemicals should be used in both the growth media and the dilution or rinse fluids. Lists of the neutralizers, the target disinfectant active ingredients, and the use concentrations have been published. Alternatively, instead of adding neutralizing chemicals to existing culture media (or if the chemical nature of the disinfectant residuals is unknown), the use of either a) commercially available media including a variety of specific and nonspecific neutralizers or b) double-strength broth media will facilitate optimal recovery of microorganisms. The inclusion of appropriate control specimens should be included to rule out both residual antimicrobial activity from surface disinfectants and potential toxicity caused by the presence of neutralizer chemicals carried over into the assay system.


Several methods can be used for collecting environmental surface samples. Specific step-by-step discussions of each of the methods have been published. For best results, all methods should incorporate aseptic techniques, sterile equipment, and sterile recovery media.

Sample/rinse methods are frequently chosen because of their versatility. However, these sampling methods are the most prone to errors caused by manipulation of the swab, gauze pad, or sponge. Additionally, no microbiocidal or microbiostatic agents should be present in any of these items when used for sampling. Each of the rinse methods requires effective elution of microorganisms from the item used to sample the surface. Thorough mixing of the rinse fluids after elution (e.g., via manual or mechanical mixing using a vortex mixer, shaking with or without glass beads, and ultrasonic bath) will help to remove and suspend material from the sampling device and break up clumps of organisms for a more accurate count. In some instances, the item used to sample the surface (e.g., gauze pad and sponge) may be immersed in the rinse fluids in a sterile bag and subjected to stomaching. This technique, however, is suitable only for soft or absorbent items that will not puncture the bag during the elution process.

If sampling is conducted as part of an epidemiologic investigation of a disease outbreak, identification of isolates to species level is mandatory, and characterization beyond the species level is preferred. When interpreting the results of the sampling, the expected degree of microbial contamination associated with the various categories of surfaces in the Spaulding classification must be considered. Environmental surfaces should be visibly clean; recognized pathogens in numbers sufficient to result in secondary transfer to other animate or inanimate surfaces should be absent from the surface being sampled. Although the interpretation of a sample with positive microbial growth is self-evident, an environmental surface sample, especially that obtained from housekeeping surfaces, that shows no growth does not represent a “sterile” surface. Sensitivities of the sampling and assay methods (i.e., level of detection) must be taken into account when no-growth samples are encountered. Properly collected control samples will help rule out extraneous contamination of the surface sample.


Source: Centers for Disease Control (CDC) and Prevention Healthcare Infection Control Practices Advisory Committee (HICPAC) “Guidelines for Environmental Infection Control in Health-Care Facilities.”


The Centers for Disease Control and Prevention (CDC) is one of the 13 major operating components of the Department of Health and Human Services (HHS), which is the principal agency in the United States government for protecting the health and safety of all Americans and for providing essential human services, especially for those people who are least able to help themselves.

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