Some considerations for anaerobic microbiology culturing

Sept. 21, 2017

Over the years, there have been many efforts to bring automation to the clinical microbiology lab in order to streamline the workflow and find alternatives to better culture anaerobes. The technological advancements have boosted the market by making microbiology tests faster, cheaper, and more accurate, and have increased the use of microbiology tests for the diagnosis of various diseases.1 Transitioning from manual to automated systems has been a challenge due to regulations and, sometimes, management resistance to change. In today’s rapidly evolving healthcare environment, management is becoming increasingly amenable to accepting change as an integral part of its function and is preparing plans to accommodate change.2

Specimen handling

Microbiology laboratories’ priorities lie in finding effective methods to select, collect, and transport a specimen in order to contribute directly to patient care. Careful selection of sites where the organism is active leads to better assessment of the disease, which then can give the test greater clinical value. Once the specimen is collected, and packed in leak-proof containers and plastic bags, it is then transported directly to the laboratory. All anaerobic samples must be submitted within 15 to 30 minutes of collection.2 The transportation of clinical specimens requires strict attention to specimen packaging and labeling instructions.3

Once samples arrive at the laboratory, time and date of receipt are recorded, and then the samples are examined to ensure they meet laboratory guidelines for testing. After the samples are approved, the laboratory selects the media type and incubation time needed based on the specimen type. The samples are than inoculated and incubated; then identification protocols, which are based on Gram stain interpretation, colony morphology, and traditional biochemical testing, are used for identifying the strain. Various vendors have developed automated systems for identification that eliminate wait time, yet most still require initial culturing.

Anaerobic culturing

A critical part of bacterial processing is creating the correct environment for non-aerobic bacteria. Anaerobic culturing requires zero percent oxygen during the entire incubation period, to guarantee a great bacterial growth yield. Technologies currently used, such as gas-paks, require up to four hours to create an anaerobic environment. The oxygen level will then be below one percent, which suggests that some of the strict anaerobes may not grow since they were exposed to oxygen during the process cycle. Other methods, such as the anaerobic chamber, will show good bacterial growth yield, but technical difficulties with the system can lead to misdiagnosis or even loss of sample. Reprocessing of samples requiring anaerobic culturing is difficult, as patient samples are either disposed of after initial culturing or held under an aerobic environment. Hence, patients are required to come back for resampling, therefore prolonging their infection and lowering their chances for fast recovery.

However, the anaerobic jar system, which uses the McIntosh and Fildes evacuation and replacement method, creates an anaerobic environment within five minutes. The method has shown a greater bacterial growth yield, allowing for accurate diagnoses. In one study, “at 24 hours, of the strains tested, 51 percent yielded larger colonies in the anaerobic jar system than in the chamber, and 30 percent yielded more growth using the anaerobic jar system than gas bags.”4

The quality and microbial test relevance depends on the accuracy of the results. Identifying the infection will help clinicians fashion the best treatment regimen. Failing to provide the correct environment for growth can lead to no bacterial growth and therefore to misdiagnoses that in some cases can be critical and lead to serious health issues. The anaerobes should not only be cultured in the appropriate conditions but transported to the laboratory in an environment thatpreserves the sample at zero percent oxygen within minutes.

The economic context

Detecting the correct microbial agents allows clinicians to prescribe the appropriate antibiotics at the right dosage, therefore minimizing the risk of antibiotic resistance, a growing health concern in the United States and globally. In addition, with today’s economic challenges, the reduction in healthcare expenditure by some governments, and rising costs related to patient care, hospitals may not have the capital to purchase an identification system that is accurate in identifying bacteria; hence the laboratory is more dependent on the anaerobic conditions. Traditional identification protocols are accurate only if the anaerobic sample is grown at the appropriate oxygen level.

Anaerobic conditioning is a challenge to hospital and reference laboratories, and management should make the decision to adopt the techniques that can eliminate the sample’s exposure to oxygen. There is a great value in adopting an automated identification system to better identify bacteria and minimize errors. To eliminate false results, laboratories can optimize their culturing mechanism by choosing a more accurate method. Use of the McIntosh and Fildes method with the anaerobic jar system has shown positive bacterial yield in comparison with other conventional methods. It not only eliminates frustration in the laboratory but minimizes identification time. Hospitals and clinicians can than focus on improving patients’ care by providing them with the correct treatment, and putting them on a faster path to recovery.


  1. Global Microbiology Testing Market (2017-2021).
  2. P.R. Murray, ed., Manual Of Clinical Microbiology. 1999: American Society of Microbiology Press. 33-35.
  3. Miller J.M. A guide to Specimen Management in Clinical Microbiology. American Society of Microbiology Press, 1996: Washington DC. National Committee for Clinical Laboratory Standards. 1989. Guidelines for Laboratory Safety, p. 11-16. CAP Environment, Safety, and Health Committee. National Committee for Clinical LaboratoryStandards, Wayne. PA.
  4. Summanen PH, McTeague M, Väisänen M-L, Strong CA, Finegold SM. Comparison of recovery of anaerobic bacteria using the Anoxomat, Anaerobic Chamber, and
    GasPak jar systems. Anaerobe. 1999:5:5-9.

Sinderella Abdallah serves as Product Manager for the Anoxomat III system, Advanced Instruments, Inc.