Interpretation of Microbiological Reports

by

Raymond B. Otero, Ph.D.
Consultant

  1. Introduction

Here you will find some examples (total of 13) of microbiological reports with interpretation. This list is certainly not complete, but it will give you some insight and helpful hints.

Before we get to the reports, there are some factors that must be explained concerning susceptibility testing. Susceptibility testing is an in vitro laboratory test method. Sometimes the results that we obtain in the laboratory does not mean it is going to work in vivo (in tissues). Table 1 lists some factors why patients do not respond to an antibiotic that the laboratory reported as susceptible. Another good example is reporting that tetracycline or ciprofloxacin is susceptible to a strain of Staphylococcus aureus that is resistant to oxacillin (MRSA). Neither one of these antibiotics should be used in a clinically infected patient with MRSA even though the laboratory reports them as susceptible. Physicians should know this.

Table 2 lists the dangers of indiscriminate use of antibiotics. We are now in an era of multi-resistant organisms. Physicians should request cultures if patient is clinically sick, and the individuals who obtain these cultures should know how to obtain them. Over use or indiscriminate use of antibiotics can lead to serious consequences as Table 2 notes.

Table 3 lists why an antibiotic is chosen over another one. Physicians and pharmacists should work with the infection control/quality review committees to make certain that antibiotics are properly prescribed.

Table 4 lists 10 steps to improve the physician's use of the laboratory. The laboratory is an excellent tool for the physician and should be used optimally.

Finally, Table 5 lists the specific types of demographics that must accompany requisition forms. We can not emphasize enough that the requisition form directs the laboratory on what to do. Incomplete forms leads to delays and possible misinterpretations.

Interpretation of Reports:

The report forms are listed and linked below. They are labeled Report Form #1, Report Form #2, etc.

Sputum specimens are difficult to obtain and often upper respiratory secretions (spit) are submitted. The health care center must recognize a good specimen from a poor one. Proper instructions must be given to the patient. The laboratory can determine if the specimen is good or bad by performing a Gram stain. The appearance of very few or non-existent WBC's and the presence of few to many epithelial cells (The purely cellular, avascular layer of cells covering the free surfaces of the mucous membrane of the mouth often referred to as stratified epithelial tissue which is composed of a series of layers with each cell varying in size and shape. Often observed when scraping of the mucous membranes of the mouth occurs or when someone "spits").

Gram stains can determine the value of the sputum specimen by examining for epithelial cells. As you can see in Laboratory Report #1, this is a "good" sputum specimen because rare epithelial cells were noted. The organism isolated was Streptococcus pneumoniae, one of the most common agent causing bacterial pneumonia. The laboratory only tests for penicillin susceptibility. In this report, this organism was susceptible to penicillin. However, we are seeing an increase number of strains that are resistant to penicillin. If the laboratory finds such resistance with a primary method (often referred to as disc diffusion or the Kirby-Bauer procedure), a second test MIC (which stands for minimal inhibition concentration) will be performed. The MIC tells the physician at what concentration the antibiotic is susceptible. This is important to the physician because he/she can use this information to determine what antibiotic would be appropriate and at what level. In this report the MIC levels were not performed (NP) which means the physician can use normal concentrations of penicillin to treat the patient.

Also observed in this report was a scant growth of respiratory flora. This is a common observation and does not take away from the significance of the report. It is not unusual to observe upper respiratory flora specifically in a scant concentration. The problem lies when a heavy growth of respiratory flora is isolated which can mask or hide the true organism of suspicion.

All health care centers should perform audits on their sputum specimens. If many of them demonstrate a moderate to high levels of epithelial cells, call the laboratory for proper inservice education on how to collect sputum specimens. The rule of thumb is "if you can not obtain it, don't send it". This is why a person who has good experience in obtaining a sputum specimen will recognize very quickly that this is not sputum but spit. Remember that the "criteria of rejection of a specimen begins on the floors of the health care center". If the laboratory rejects it, or the Gram stain indicates that the specimen is poor, the physician can not help his/her patient.

Remember that the laboratory will not perform or report the Gram stain result unless the health care orders it on a requisition form. The Gram stain report should accompany the culture findings. For example, if the Gram stain report demonstrates that the sputum specimen obtained is a good specimen, and only upper respiratory flora was isolated, then the physician can rule out bacterial pneumonia with common organisms. He/she still has to think about viral, mycotic or possible tuberculosis pneumonia. If the Gram stain reports that the specimen is spit (see Laboratory Report #7), then time was lost and the physician is back to "square one". The nursing staff have a tremendous responsibility in making sure that the specimen was obtained correctly in the first place.

The gram stain report indicates numerous WBC's which implies this patient is infected with Enterococcus faecalis. The gram stain also picked up the organism - gram positive cocci in chains. Notice that this strain of E. faecalis is resistant to vancomycin (VRE). CDC back in the Fall of 1994 wrote a document alerting healthcare facilities that strains of E. faecalis were developing resistance. Nurses who receive microbiology reports demonstrating VRE need to call the physician for this patient as soon as possible.

There are four areas on a report form (see Table 5) that nurses should examine:

  1. Source - to make certain that the nurses on the staff are writing the appropriate source correctly;

  2. Gram stain report - to see if WBC's are present indicating infection;

  3. Organism - often indicates possible source (i.e., Escherichia coli isolated from urine specimens may indicate indigenous contamination from the perineal region causing infection);

  4. Antibiogram - demonstrates what antibiotics are resistant or susceptible to certain antibiotics (e.g., If you examine Laboratory Report #3, you will see that this strain of Staphylococcus aureus is resistant to oxacillin (methicillin = MRSA).

Since this patient is infected (Note gram stain report = numerous WBC) with MRSA, only one antibiotic can be used for treatment and that is vancomycin IV. Even though other antibiotics demonstrate susceptibility (tetracycline and trimethoprim-sulfa), they can not be used to treat an infected patient.

The physician should be called immediately. The possibility of isolation may be based on the following situations:

  1. patient's drainage can not be normally contained with dressing;

  2. patient's hygiene is very poor;

  3. patient's mental status is such that contamination of other residents is a distinct possibility;

  4. patient is compromised with other conditions (i.e., diabetes, immunologically compromised, cancer, etc.);

  5. staff members are simply not understanding the epidemiology of MRSA and therefore segregation (isolation) of the resident is imperative to avoid dissemination.

This patient is infected with Pseudomonas aeruginosa. Colony count indicates greater than (>) 100,000 CFU/ml (CFU = colony forming units - number of colonies counted on a culture plate). Usually this concentration (>100,000 CFU/ml) on a clean catch urine is significant. The organism, Ps. aeruginosa, is resistant to all antibiotics tested. The physician should be alerted as soon as possible. This patient may need to be isolated if the conditions seen in Laboratory Report #3 are observed. If this organism infects the skin, it would be very difficult to achieve proper serum levels (Table 3). The nurses on staff should examine this patient on a routine basis for breakdown in skin tone.

Streptococcus pyogenes is the major cause of pharyngitis in humans. Unless the laboratory is told to examine for other organisms (e.g. Bordetella pertussis [whooping cough], Neisseria gonorrhea, Candida sp. [yeast], Hemophilus influenzae), no other organism will be identified. This organism has yet to demonstrate resistance to penicillin in the United States.

This specimen was grossly contaminated by indigenous flora of the external genitalia. It is important for the health care facilities to make certain that urine specimens are properly collected. Health care facilities should perform retrospective studies (perhaps the last 30 days or specimens) on urine specimens to see how well they are doing. Check with the laboratory if questions arise on how to collect urine specimens.

As Laboratory Report #1 indicated, the presence of numerous WBC’s and few epithelial cells demonstrated that an acceptable specimen was submitted for culture. However, as you can see in Report #7, this was not the case. Numerous epithelial cells seen on the Gram stain indicates upper respiratory secretions or "spit". Sputum specimens are difficult to obtain if the patient is not given proper instructions. Call your laboratory to help you in developing in-service educational seminars on specimen collection and transport.

Laboratory Reports #4 and #8 are examples of a multi-resistant bacterial strains cultured in urine. What creates this scenario is the over use of antibiotics in healthcare facilities. Physicians should be careful in treating asymptomatic patients thus creating the "superbug".

This urine sample demonstrated no growth. No viable organisms were cultured on this specimen. If the patient was on antibiotics, the laboratory needs to know this information. The urine specimens containing antibiotics may be handled differently by the microbiology laboratory. Urinalysis should be performed on all urine specimens submitted. If the urinalysis is negative, why perform a culture.

We are assuming that this patient had an eye drainage (infection), hence the reason for the culture. There were no significant bacterial organisms isolated from this specimen. This could be due to two factors:

  1. eye infection may have been due to a viral agent;

  2. specimen was taken and/or transported improperly

  3. irritation of the eye by some other mechanism other than bacterial.

Check with the laboratory when you receive such a report. It would be wise to submit two swabs for examination from this site, one for culture and one for a gram stain. Also it would be wise to submit a culture from the good eye for comparison of indigenous flora that may be present. Make certain if you do the latter, that you mark the requisition form(s) left eye and right eye.

The laboratory only cultures for Salmonella, Shigella, and Campylobacter sp., Yersinia sp., and Vibrio sp. are only cultured upon request. Usually if a stool culture is submitted for enteric pathogens, the probability that the infection occurred in the community rather than in a health care facility is very high. However, there are exceptions to this if one reads CDC's weekly reports. A negative bacterial stool culture may also indicate a viral gastroenteritis.

This is an example of colonization and not an infection (no WBC's). Probability indigenous contamination from fecal origin. Note that this organism, Escherichia coli, is susceptible to all antibiotics tested. This indicates that it is not a hospital/nursing home strain, otherwise some resistance would have been observed.

The physician is trying to rule out tuberculosis. However, as you can see acid-fast organisms were observed on the smear. Acid-fast stains are used to detect Mycobacterium organisms in specimens such as lower respiratory specimens (sputum), lung biopsies, bronchial washings. Acid-fast means that the organism, Mycobacterium, can not be decolorized with acid alcohol (ethyl alcohol-hydrochloric acid combination) and the organism retains the primary dye (carbol fuchsin, or auramine). It is important for the health care worker to understand that the presence of acid-fast organisms on a smear indicates infectivity of the patient and warrants tuberculosis control (proper masks, private room with air exchanges and negative pressure).

  1. Summation

If you have any questions concerning these reports, please call your reference laboratory. One other point I would like to mention is as you examine these reports you will notice that similar antibiotics were observed for Gram negative, non-urine, Gram negative, urine and Gram positive organisms. Table 6 lists reasons for not routinely testing and reporting numerous drugs. Physicians must be made aware of this. Like everything else in life, we are controlled by the federal government on what antibiotics we can use for testing. Hopefully Table 6 will give you many reasons why we are under specific controls.

 

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