Identifying Causative Agents

When a patient presents with a known infection, or symptoms suggestive of an infection, it is important to identify the causative agent as soon as possible to prevent misdiagnosis, unnecessary treatment, inconvenience and possibly higher healthcare costs.

In most bacterial infections, for example, practitioners may initiate empirical treatment in the interest of time and to satisfy patient demand.

However, in order to effectively treat that condition they must rely on the identity of the agent, and on its susceptibility to certain pharmaceutical agents like an antibiotic. It requires this specificity of information to customize treatment.

Treatment with a less efficacious antibiotic spells increased expenses and prolongation of the infection. Even overuse of powerful broad spectrum antibiotics may help to promote antibiotic resistance.

The Infectious Diseases Society of America and the American Society of Microbiology joined forces to publish a guide to help physicians minimize the problems associated with laboratory testing to diagnose infectious diseases.

While these guidelines are directed at physicians, nurses also play a pivotal role in specimen collection, often acting as gatekeepers and advisors as they remind other clinicians of the correct protocols.


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Proper Identification

The need to identify infectious agents occurs in various settings: primary care, specialty care, emergency department, in hospitals and even in outpatient settings.

Both sponsoring organizations and the authors of the guidelines conceded that not all physicians are familiar with proper test selection, specimen collection and storage, or interpretation of results related to infectious diseases.

Ellen Jo Baron, PhD, a lead author of the guide and professor at the Stanford School of Medicine in Stanford, Calif., said she has been receiving feedback that this guide was “badly needed.”

While ID specialists are likely to be very knowledgeable, most other providers might not have the time or interest to keep up with changes, some of which are slight and nuanced, in medical laboratory diagnostics.

Baron added that this guide will be made available through apps so that physicians can access the information on their smart phones and other electronic devices like tablets. Laminated cards containing key elements of the guide are also available for posting in clinical settings. These cards can be customized to the setting based on population and disease incidence.

Divide & Conquer

The guide is divided into sections based on anatomic sites and body systems, including blood stream, cardiovascular system, eyes, soft tissue of the head and neck, upper and lower respiratory system, gastrointestinal tract, abdomen, bone and joints, urinary tract, genitals and so on. It can also be accessed in terms of specific infections: bacterial, viral, tick-borne and parasitic.

Based on the suspected agent (and the site), the physician is prompted to order the most appropriate test, is guided on the correct specimen, the collection device, storage conditions (time and temperature) and ideal transport procedures. Precautions on avoiding common errors – and actions that will make a specimen unacceptable by the laboratory- are listed for most tests.

Nothing is more frustrating than having a hard to obtain specimen rejected by the laboratory. Medical laboratories have very specific policies for accepting or rejecting specimens based on regulatory guidelines and scientific rationales which are not necessarily logical or intuitive to clinicians.

Something as “simple” as a non-refrigerated urine specimen, using the wrong type of swab, a partially labeled specimen, swabbing a site instead of sending a piece of infected tissue might all be reasons for rejection because they will provide incomplete or even erroneous result on which clinical decisions might subsequently be made.


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Specimen Mangement

The guide lists 10 basic rules of specimen management for proper patient care.

1. Specimens of poor quality (including incorrect specimen for the test required) will be rejected because of the risk of compromised results. Recollection might be inconvenient or even impossible. It is important to collect the right specimen the first time. Obtain proper collection devices from the lab if necessary. Do not improvise.

2. Do not demand a result of “everything that grows.” Depending on the quality of the specimen and the growth media used in the lab, contaminants and clinically insignificant organisms may grow. Rely on the expertise of the medical lab scientist in the laboratory to follow clinical protocol when reporting results based on the anatomical site and the specimen type.

3. Avoid contamination of specimens. Careful collection is key to avoiding contamination with extraneous material including from adjacent sites. For example if the collector is not careful a throat swab can be easily contaminated by skin and mouth bacteria from the teeth, gums and cheek. Recovery of these organisms may confuse the diagnosis at best.

4. Actual tissue, aspirates and fluids are usually the specimens of choice. A swab may not hold enough of the infected material to get a good growth. Some materials also cling to the swab and are hard to dislodge in the lab. However, swabs are sometimes acceptable (and even preferable) e.g. throat, nasopharyngeal, and viral respiratory infections.


Infection Control

By following infection control principles you will create a safe environment for you, your co-workers and your patients.

5. Laboratory protocols for rejection and reporting are based on clinical practice guidelines and standards of care and are not simply whimsical.


6. Always collect your specimen before starting antibiotics.

7. Susceptibility (sensitivity) testing should be performed on clinically significant organisms, not on every organism that grows from the specimen submitted.

8. Laboratory results should reflect the nature of the infection accurately: right patient, body site, actual causative agent, clinically relevant.

9. The clinical laboratory-not medical staff- should set technical policy. Good communication and mutual respect will guide policy and will help to answer confounding clinical questions that are not “run of the mill.”

10. Specimens must be labeled accurately and completely so as to be distinct from all others. Labeling should include patient’s full name, medical record number or date of birth, and the collection site, including side of body if appropriate. Example: “Brown, John. DOB 4-5-73. Dog bite wound, left calf. Collected 9-2-13 by Dr P Jones” Labels should be placed directly on the actual specimen container and not on any outer transport container like a biohazard bag.

By following these simple rules the clinician can ensure that the correct specimen is collected every time and submitted to the clinical laboratory in a viable condition. The results they receive from the lab will be more meaningful and useful.

In the end, if you follow these guidelines, your clinical laboratory will thank you; but more importantly, your patient will thank you.

Glen McDaniel is a healthcare executive, clinical lab scientist, speaker and freelance writer. His interests include mediation, leadership, change and ethics. He can be reached at

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