Acid-fast bacteria, also known as acid-fast bacilli or simply AFB, is a group of bacteria sharing the characteristic of acid fastness. Acid fastness is a physical property that gives a bacterium the ability to resist decolorization by acids during staining procedures. This means that once the bacterium is stained, it cannot be decolorized using acids routinely used in the process. This important and unique feature of certain bacteria gives us the ability to classify and detect them using relatively easy laboratory procedures such as microscopy. Bacteria displaying acid fastness include:
Acid fastness can also be attributed to other structures not classified as bacteria. These include:
Even though acid fastness can be attributed to many different bacteria, in clinical practice, correlation with history makes it a fairly unique characteristic of M. tuberculosis. This makes acid-fast staining sensitive and specific, provided clinical correlation is part of the equation. This writing will focus on the acid-fast bacteria M. Tuberculosis. The diagnosis of M. Tuberculosis using this characteristic is referred to as TB microscopy, acid-fast smear microscopy, and direct sputum near microscopy. Even though the use of highly advanced molecular diagnostic tests have come into play, the value of this staining technique cannot be overstated, especially, for low and middle-income countries.
M. Tuberculosis is primarily a pathogen of the lung, therefore, for all types of tuberculosis, the primary specimen required in acid-fast smear microscopy is sputum. There are 4 chief ways of collecting sputum.
Sputum collection must be performed in dedicated areas that are well ventilated to prevent the nosocomial inhalation of aerosols by uninfected people. Purulent and mucopurulent sputum are considered good specimens for microscopy. Suboptimal samples include mucoid, mucosalivary, and salivary specimens. It is important to differentiate salivary sputum specimens from saliva and mucus, as the latter are not representative of lung status and may give false-negative results. The presence of food debris and contaminants is not advised, however, blood-tinged or bloodstained sputum is considered acceptable. Medical laboratory personnel should also regularly evaluate specimen quality before performing TB microscopy.  Patients must be requested to repeat the collection until an acceptable specimen is achieved. Besides the quality, the amount of the specimen is also important and should be a minimum of 5 milliliters.  Inadequate volume affects the sensitivity of the test, thus reducing its medical utility.
Sputum specimens must be collected in appropriate containers. A 50-ml plastic, screw-capped, transparent container is usually used to foster a secure containment. The transparency of the container allows for visual inspection of the specimen to assess its consistency and quality. Appropriate labeling of the sample with the patient’s name and date of the collection must be ensured. The collected sample should be stored at 2 to 8°C until transported to the laboratory. According to the American Centers for Disease Control and Prevention, at least 3 consecutive sputum samples, each collected at 8 to 24-hour intervals, with at least one sample being an early morning expectorate, are required for diagnosis. In those countries with an established and well-implemented external quality assessment (EQA) program but limited human resources, the World Health Organization recommends using two specimens for diagnosis. This is to facilitate the early or “same day” diagnosis of tuberculosis patients from the community.
Microscopic evaluation of sputum for acid-fast bacilli begins with making a smear. A typical smear is 3 cm by 2 cm in size, however, depending on the individual laboratory guidelines, it can be as small as 2 cm by 1 cm as well. Smearing must be done by pressing and applying the sputum uniformly on the slide. Ideally, a smear of uniform thickness should be made at the center of the slide to facilitate visualization using a microscope. The smeared slides should also be properly heat-fixed before proceeding on to the staining process. Training staff to make good smears is pivotal for accurate and valid testing. 
Acid-fast structures can be visualized under a microscope using two principal methods, the carbolfuchsin staining, and the fluorochrome procedure.
The carbolfuchsin staining comprises of the Ziehl-Neelsen method and the Kinyoun method. In the Ziehl-Neelsen method, smeared slides are first stained with carbolfuchsin (CF).  This is done by submerging the smear in a drop of carbolfuchsin and subsequently heating it using an alcohol lamp until steam can be seen rising. This facilitates the penetration of the stain inside each bacterium. Care must be taken that boiling does not occur as that may alter the results of the test. The stain and smear should remain in contact for approximately 10 minutes and be allowed to cool down thereafter, thus, trapping the stain within the bacterial cell wall. These steps make the entire smear, including acid-fast bacilli, red. After stain fixation, the second step focuses on washing the excess stain off from the smear. This is done by gently washing the smear in a stream of water and then covering it with acid alcohol for 2 to 3 minutes. Acid alcohol has the ability to completely decolorize all non-acid-fast organisms, thus only leaving behind red-colored acid-fast organisms, like M. Tuberculosis. The slides are then stained a second time with methylene blue that serves as a counterstain. The recommended time for stain to smear contact is 1 minute but is largely dependant on the quality of methylene blue. Counterstaining creates an effective visual contrast of red acid-fast bacilli during microscopy. The Ziehl-Neelsen method of staining is also called the hot method as it involves heating the carbolfuchsin stain. In contrast the historic method of staining called the Kinyoun method does not involve heating and is hence known as the cold method.
The fluorochrome procedure primarily utilizes one of two dyes, the auramine-O dye, or the auramine-rhodamine dye. Auramine-O is a hydrochloride dye which causes stained AFB to emit fluorescence (green or yellow) when viewed under a fluorescence microscope. Unlike the Ziehl-Neelsen method, heating is not required for penetration of the stain into the bacteria. The stain to smear contact time, however, must be a minimum of 20 minutes for the acid-fast organisms to pick up the stain properly. After the auramine dye has fully stained the smear, a drop of acid alcohol is applied for one to two minutes to decolorize the smear. Methylene blue or potassium permanganate is used as a counterstain to provide a background color. Potassium permanganate is preferred as it provides a darker background giving it a better contrast and sensitivity as compared to methylene blue.  The last step is to gently wash the slide with slow running water and letting it dry. Blotting the slide is avoided as it may damage the stained smear.
Multiple studies have compared the Ziehl-Neelsen method with the fluorochrome procedure. The results obtained by both methods are considered highly reproducible. This means that both methods are equally capable of detecting acid-fast bacilli in a sputum sample.  Although, it is interesting to note that a few studies suggest that fluorescence microscopy is more likely to positively detect a sputum sample with a fewer number of acid-fast bacilli. It also has the advantage of taking half as long as light-microscopy to declare a sample negative of acid-fast bacilli. 
AFB-microscopy is indicated for suspected cases of tuberculosis. Positive microscopy confirms the presence of acid-fast bacilli. Care must be taken not to interpret positive results as M. tuberculosis because the Ziehl-Neelsen stain only indicates the presence of acid-fast bacteria/structures. Other acid-fast organisms for which Ziehl-Neelsen stain may test positive are mentioned in the introduction.
The result of acid-fast microscopy must always be clinically correlated with the patient’s history, examination, and other relevant investigations.  Acid-fast microscopy is an effective and reliable tool for monitoring the patient's response to therapy. For a patient of tuberculosis, the confirmation of cure is established by negative acid-fast microscopy at the end of the treatment regimen. Similarly, the infectivity of a tuberculosis positive patient can also be assessed via sputum microscopy. On the other hand, multidrug-resistant tuberculosis and extremely drug-resistant tuberculosis cannot be differentiated from susceptible M. tuberculosis via this technique. Identification of these strains requires specific and sensitive investigations such as culture and drug susceptibility tests (DST).
In some settings, the Xpert MTB/Rif assay, a nucleic acid amplification test (NAAT), has replaced sputum microscopy as a primary tool of diagnosis.  Having said that, monitoring the progression of the disease using this molecular technology has not been found effective and thus, even in those settings, the importance of acid-fast microscopy still stands. 
Reading smears is a critical step in sputum microscopy. The Global Laboratory Initiative (GLI) handbook for acid-fast microscopy specifies guidelines for reading, recording, and reporting results for both, Ziehl-Neelsen and auramine method.  The recommended number of visual fields to be examined is 150 for a smear size of 3 cm x 2 cm and 100 for a smear size of 2 cm x 1 cm. It should however be noted that some countries have their own guidelines for interpreting and reporting results. The results of acid-fast microscopy may be reported according to the following standards:
Even though the sensitivity and specificity of Ziehl-Neelsen stain for pulmonary tuberculosis can be up to 70% and 97.1% respectively, several factors can interfere with accurate and valid reporting of results.
Pre-analytical factors such as wrongly labeling the sample, inappropriately storing, and transporting the specimen and poor technique for sample collection can all result in a discrepancy of the microscopy results. Sample for sputum microscopy must be expectorated from the lungs, failure to do so may significantly affect the sensitivity of this test as well. Exposure to direct sunlight and excessive heat can also destroy a significant number of acid-fast bacilli in the sputum sample, thereby rendering the results compromised.
Analytical factors such as poor smearing, staining, and microscopy can also hamper the results of acid-fast microscopy. Appropriate smearing requires correct smear size, thickness, and fixation. Improper staining of the slides can be caused by slide contamination, incorrect staining time, over or under-heating the stain, and blotting the smear with paper for drying.  The report of microscopy is also dependent on the microscope itself and the person analyzing the sample. The reported number of bacilli can differ from person to person, and therefore, proper training is also essential for accurate and valid results.
Post-analytical factors can involve mix-up and release of mismatched patient results and other clerical mistakes. Long turnaround time and an incorrect result interpretation can also potentially hinder the use of acid-fast microscopy as a diagnostic tool. 
False-positive and false-negative results of acid-fast microscopy may have grave repercussions on the patients individually and also the society as a whole. False-positive results (i.e. a positive result for an actually negative patient) will result in unnecessary treatment with anti-tuberculosis drugs. These drugs can cause significant side effects ranging from mild elevation in liver enzymes to full-blown hepatic failure. Optic neuritis, color blindness, and peripheral neuropathy are just some of the other potential side effects of anti-tuberculosis medicines. 
False-positive results can be a result of:
On the other hand, false-negative results (i.e. the patient has tuberculosis but receives a negative report) will result in improper management of the patient leading to exacerbation of the disease and community spread.
False-negative results can result from:
Acid-fast bacilli microscopy poses a threat to the laboratory personnel as well. Pathologists working in the laboratory are at risk of acquiring tuberculosis infection if proper guidelines are not followed. Handling samples and smear processing must be done with extreme caution so that tuberculosis is not transmitted inadvertently. The Good Clinical Laboratory Practice standards require all labs handling M. tuberculosis to have:
Furthermore, access to the lab must be restricted and all samples must be stored appropriately in a Class II Biosafety cabinet.
The stigma of tuberculosis still exists.  The value of patient education regarding the disease and the possibility of treatment and cure is critical. Patients must be educated about easier, cheaper, and yet, reliable ways of diagnosing pulmonary tuberculosis using acid-fast microscopy. Since acid-fast microscopy is non-invasive, patients feel comfortable getting tested. Knowledge of the availability and access to an accurate and reliable diagnostic tool such as acid-fast bacilli microscopy can build the patient's trust and confidence in healthcare providers. 
Acid-fast microscopy remains a valuable laboratory test for diagnosing and screening patients of active pulmonary tuberculosis. This technique is relatively inexpensive and requires little training and expertise. For middle- and low-income countries, acid-fast microscopy provides a cost-effective alternative to the expensive nucleic acid amplification tests. Furthermore, the infectivity of tuberculosis patients can also assessed by this tool. Considering the high burden of tuberculosis and the need for a fast, safe, inexpensive, sensitive and specific diagnostic test, acid-fast microscopy, whether by fluorescence staining or carbolfuchsin staining, remains a standard of care.
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