[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"$fxLN3MUwXCdr5RPjwZYIDpOj8CHyjOmngWTgoKXPtZbg":3,"$fwAHjVv7gGCPN10FclT7VHopC7jB3a9Kn0BkZl0sB6i8":32,"$f3Ft0rKFJHppdzE-vuveecxx1BUcg9iOlMLtyzf_MJDg":165},[4,8,12,16,20,24,28],{"title":5,"slug":6,"path":7},"About Microbeonline.com","about-microbeonline-com","\u002Fabout-microbeonline-com\u002F",{"title":9,"slug":10,"path":11},"About Me","about-me","\u002Fabout-microbeonline-com\u002Fabout-me\u002F",{"title":13,"slug":14,"path":15},"Advertise with Us","advertise-us","\u002Fadvertise-us\u002F",{"title":17,"slug":18,"path":19},"Privacy Policy","privacy-policy","\u002Fprivacy-policy\u002F",{"title":21,"slug":22,"path":23},"Abbreviations","abbreviations","\u002Fabbreviations\u002F",{"title":25,"slug":26,"path":27},"Microbes","microbes","\u002Fmicrobes\u002F",{"title":29,"slug":30,"path":31},"Books","recommended-books","\u002Frecommended-books\u002F",{"type":33,"data":34},"blog",{"slug":35,"title":36,"description":36,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":39,"lastUpdatedDate":40,"draft":41,"category":42,"image":37,"body":43,"faq":44,"tags":45,"related":47},"introduction-transmission-pathogenesis-and-lab-diagnosis-of-leprosy-hansens-disease","Leprosy: Etiology, Pathogenesis, Lab Diagnosis",null,"Acharya Tankeshwar","2012-05-15","2026-07-04",false,"bacteriology","Leprosy is an age-old disease, associated with social stigma; historical records and literature show that people afflicted with leprosy have often been ostracized by their communities and families. Also known as Hansen’s disease, leprosy is a chronic infectious disease caused by an acid-fast bacillus, *Mycobacterium leprae*.\n\n![ - A man with leprosy (image by J. L. Losting.)](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FA-Man-with-a-leprosy-Image.jpg)Figure: A man with leprosy (image by J. L. Losting.)\n\nIn 1873, [Dr. Hansen](https:\u002F\u002Fen.wikipedia.org\u002Fwiki\u002FGerhard_Armauer_Hansen) discovered bacteria in leprosy lesions, which rule out that leprosy is a hereditary disease not a punishment from the gods. Leprosy mainly affects the skin, peripheral nerves, and mucosa of the upper respiratory tract (because their **optimal temperature for growth is 30°C**). It may affect many organs.\n\n## Features of M. Leprae and Leprosy\n\n1. Leprosy is not a highly infectious \u002Fvery contagious infection.\n2. Infection is acquired by **prolonged contact with patients with lepromatous leprosy (heavy shedders)** who discharge *M. leprae* in large numbers in nasal secretions and from skin lesions.\n3. Route of Transmission: Skin and inhalation.\n4. *M. leprae* multiplies very slowly (with a doubling time of 14 days; slowest growing human bacterial pathogen).# Remember: antibiotic therapy must be continued for a long time, usually 1-2 years.\n5. Incubation period of the disease is about five years. Symptoms can take as long as 20 years to appear.\n6. Leprosy is curable with multidrug therapy (MDT). Three antibiotics (dapsone, rifampicin, and clofazimine) in combination are used for 6 months to 1 year based on the type of leprosy (paucibacillary or multibacillary).\n\n## Pathogenesis\n\n*M. leprae* replicates intracellularly, typically within skin **histiocytes**, endothelial cells, and the **schwann cells** of nerves. Cell-mediated immunity (CMI) plays a major part in determining the response of the host to leprosy.\n\n![Pathogenesis of Leprosy](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FPathogenesis-of-Leprosy-1.jpg)Figure: Pathogenesis of Leprosy\n\nThere are two distinct forms of leprosy-tuberculoid and lepromatous with several intermediate forms between the two extremes\n\n1. **Tuberculoid leprosy:** very few acid-fast bacilli in skin smear (paucibacillary disease): Cell-mediated immune (CMI) response is adequate and the lepromin test is positive.\n2. **Lepromatous leprosy:** large numbers of *Mycobacterium leprae* chiefly in masses within the lepra cells, often grouped together like bundles of **cigars or arranged in a palisade** (multibacillary disease). The cell-mediated immune  (CMI) response to the organism is poor and the lepromin test is negative.\n\n## Ridley and Jopling Classification\n\nRidley and Jopling (1966) have introduced a scale for classifying the spectrum of leprosy into five groups:\n\n1. Tuberculoid (TT)\n2. Borderline Tuberculoid (BT)\n3. Borderline (BB)\n4. Borderline Lepromatous (BL)\n5. Lepromatous (LL)\n\n## WHO Classification of Leprosy\n\nAccording to World Health Organization (WHO), leprosy is divided into two groups, **paucibacillary and multibacillary**.\n\n**Comparison of tuberculoid and  lepromatous leprosy**\n\n\u003Ctable style=\"min-width: 75px;\">\n\u003Ccolgroup>\u003Ccol style=\"min-width: 25px;\">\u003Ccol style=\"min-width: 25px;\">\u003Ccol style=\"min-width: 25px;\">\u003C\u002Fcolgroup>\u003Ctbody>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>\u003Cstrong>Feature\u003C\u002Fstrong>\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>\u003Cstrong>Tuberculoid\u003C\u002Fstrong>\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>\u003Cstrong>Lepromatous\u003C\u002Fstrong>\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Type of lesion\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>One or few lesions with little tissue destruction\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Many lesions with marked tissue destruction\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Number of acid-fast bacilli\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Few\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Many\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Likelihood of transmission\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Low\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp> High\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Cell-mediated response \u003Cem>to M. Leprae\u003C\u002Fem>\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Present\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Reduced or latent\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Lepromin skin test\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Positive\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Negative\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003C\u002Ftbody>\n\u003C\u002Ftable>\n\n## Laboratory diagnosis\n\n### Sample\n\n![M. leprae in stained smear  - M. lepraein stained smear](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FLeprosy-bacillus.jpg)Figure: M. lepraein stained smear\n\nIdeally, at least six sites can be sampled, including **earlobes, eyebrows, elbow, knees, nasal mucosa,** and skin lesions. Skin biopsy from edges of active patches and nerve biopsy from thickened nerves can also be collected.\n\n### Taking a skin smear for the diagnosis of Leprosy\n\nTraditionally smears used to be taken from four or even six sites, but two sites are now considered adequate in most cases. **Skin smear is taken from one ear lobe and one lesion**. Smear should be taken from the edges of the most active lesions (active lesions are raised and reddish in color). If there is no suitable skin lesion, a second smear can be taken from another ear lobe.\n\nTo take a skin smear, the following equipment will be needed\n\n![Equipment needed to take skin smear](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FEquipments-needed-to-take-a-skin-smear.png)Figure: Equipment needed to take skin smear\n\n- Gloves\n- Swab and spirit\n- Scalpel handle and new blades\n- Dressing strips\n- Safe disposal for used blades\n- Spirit lamp\n- Slide box and new slides\n\n**Procedure**\n\n![](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FTaking-a-skin-smear.jpg)\\- Wash your hands **(1)** and put on gloves.\n\n- Take a new, clean, unscratched microscope slide. Using a slide marker, write the patient identification (ID) number at the bottom of the slide **(2)**. This number must be on the request form.\n\n- Clean the skin at the smear sites with a cotton wad drenched in alcohol. Let it dry.\n\n- Light the spirit burner.\n\n- Put a new blade on the scalpel handle. If you put the scalpel down, make sure the blade does not touch anything.\n\n- Pinch the skin firmly between your thumb and forefinger; maintain pressure to press out the blood.\n\n- Make an incision in the skin about 5 mm long and 2 mm deep **(3)**. Keep on pinching to make sure the cut remains bloodless. If bleeding, wipe the blood away with cotton wad.\n\n- Turn the scalpel 90° and hold it at a right angle to the cut.\n\n- Scrape inside the cut once or twice with the side of the scalpel, to collect tissue fluid and pulp. There should be no blood in the specimen, as this may interfere with staining and reading.\n\n- Stop pinching the skin and absorb any bleeding with a wad of cotton. Spread the material scraped from the incision onto the slide, on the same side as the ID number. Spread it evenly with the flat of the scalpel, making a circle 8 mm in diameter **(4).**\n\n- Rub the scalpel with a cotton wad drenched in alcohol. Pass the blade through the flame of the spirit burner for 3 to 4 seconds. Let it cool without touching anything. Repeat the steps above for the second site. Spread this smear next to, but not touching, the first one.\n\n- Discard the scalpel blade safely. Dress the wounds and thank the patient.\n\n- Let the slide dry for 15 minutes at room temperature, but not in direct sunlight.\n\n- Fix the smears by passing the slide, with the smears upwards, slowly through the flame of a spirit burner, 3 times **(5).** Do not overheat. The slide should not be too hot to touch.\n\n- Put the slide in a slide box and send it to the laboratory with the skin smear request form.\n\n### Microscopy\n\nSlit-skin smear is stained with a **modified Ziehl Neelsen stain** (5% sulphuric acid or 1% v\u002Fv acid alcohol is used as a decolorizing agent). Find [details about Ziehl-Neelsen stain procedure here](\u002Fziehl-neelsen-technique-principle-procedure-reporting\u002F). Stained slides are observed under a microscope (100x objective lens using immersion oil).\n\n*M. leprae* is a slightly curved filament 3-10 m in length containing irregular arrangements of dense material sometimes in the shape of rods. Acid-fast bacilli appear as fine red rods against a blue background. They can be straight or curved, and the red color can be uniformly distributed (solid bacilli) or unevenly distributed (fragmented and granulated bacilli). Clumps of bacilli are called globi. Solid bacilli may suggest the presence of viable organisms and may be seen in new, untreated cases or in relapse cases. Bacilli which stain irregularly are probably dead and degenerating.\n\n![AFB (M. leprae) in skin smear  - AFB in skin smear](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FAFB-in-Skin-Smear.png)Figure: AFB in skin smear\n\n- **In lepromatous leprosy:lipid-laden macrophages called‘foam cells”** containing **many acid-fast** bacilli are seen in the skin.\n- **In tuberculoid leprosy**: Very few acid-fast bacilli are seen and the appearance of typical granulomas is sufficient for diagnosis.\n\nBased on the number of *M. lepare* and their morphology in the stained slides **Bacteriological index (BI)** and **morphological index (MI)** can be calculated. **Bacteriological index (BI)** is an expression of the extent of bacterial loads whereas **morphological index (MI)** is calculated by counting the numbers of solid-staining acid-fast rods *(viable during sample collection)*.\n\n**BI** and **MI** are useful in assessing the amount of infection, the viability of the organisms, and also the progress of the patient under treatment.\n\n\u003Ctable style=\"min-width: 50px;\">\n\u003Ccolgroup>\u003Ccol style=\"min-width: 25px;\">\u003Ccol style=\"min-width: 25px;\">\u003C\u002Fcolgroup>\u003Ctbody>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>\u003Cstrong>Grading\u003C\u002Fstrong>\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>\u003Cstrong>Bacteriological Index (BI)\u003C\u002Fstrong>\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>0\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>Absence of AFB in 100 fields\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>1+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>1-10 AFB\u002F100 fields\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>2+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>1-10 AFB\u002F10 fields\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>3+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>1-10 AFB\u002Ffield, on average, in each field\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>4+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>10-100 AFB, on average, in each field\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>5+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>100-1000 AFB, on average, in each field\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003Ctr>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>6+\u003C\u002Fp>\u003C\u002Ftd>\u003Ctd colspan=\"1\" rowspan=\"1\">\u003Cp>>1000 AFB, on average, in each field\u003C\u002Fp>\u003C\u002Ftd>\u003C\u002Ftr>\u003C\u002Ftbody>\n\u003C\u002Ftable>\n\nAccording to WHO, a more accurate and reliable index of the bacillary content of a lesion is given by the **logarithmic index of biopsies (LIB).** These indices help to assess the state of patients at the beginning of the treatment and to assess progress.\n\n> Patients with lepromatous leprosy may give false-positive results in the nonspecific serologic tests for syphilis, such as VDRL and RPR.\n\n![Nine banded armadillo - Nine-banded armadillo](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FNine-banded-armadillo.jpg)Figure: Nine-banded armadillo\n\n### Culture\n\n*M. leprae* has not yet been successfully cultured in vitro (either on artificial media or in cell culture) but it can be grown in the laboratory by injection into the footpads of mice or nine-banded armadillo. It is a slow-growing pathogen with a doubling time of 14 days.\n\n### Serology\n\nA serologic test for [IgM ](\u002Figm-antibody-structure-properties-functions-clinical-significance\u002F)against phenolic glycolipid-1 is useful in the diagnosis of lepromatous leprosy but not useful in the diagnosis of tuberculoid leprosy.\n\n### Molecular diagnosis\n\n[Polymerase Chain Reaction (PCR)](\u002Fpolymerase-chain-reaction-pcr-steps-types-applications\u002F) can be used as a means of diagnosis of leprosy and also as a tool for drug assessment.\n\n### Lepromin Skin Test\n\nThe lepromin skin test is **not used to diagnose leprosy** but to determine what type of leprosy a person has. Lepromin skin test is similar to [tuberculin test.](\u002Ftuberculin-skin-test-mauntoux-testprinciple-procedure-results-limitations\u002F)  An extract of *M.leprae* is injected intradermally and induration is observed 48 hours later in those in whom a cell-mediated immune response against the organism exists.\n\nThe lepromin test is employed mostly for the following two purposes.\n\n1\\.       To classify the lesions of leprosy patients.\n\n2\\.       To assess the prognosis and response to treatment.\n\n**References and further reading**\n\n1. Chimenos Küstner, E., Pascual Cruz, M., Pinol Dansis, C., Vinals Iglesias, H., Rodríguez de Rivera Campillo, M. E., & López López, J. (2006). Lepromatous leprosy: a review and case report. *Medicina oral, patologia oral y cirugia bucal*, *11*(6), E474–E479.\n2. Bhandari, J., Awais, M., Robbins, B. A., & Gupta, V. (2023). Leprosy. In *StatPearls*. StatPearls Publishing.\n3. Britton, W. J., & Lockwood, D. N. (2004). Leprosy. Lancet (London, England), 363(9416), 1209–1219. \u003Chttps:\u002F\u002Fdoi.org\u002F10.1016\u002FS0140-6736(04)15952-7>",[],[46],"mycobacteria",[48,56,65,110,127,133,150,157],{"slug":49,"title":50,"description":50,"seoTitle":37,"seoDescription":37,"author":51,"createdDate":52,"lastUpdatedDate":53,"draft":41,"category":42,"image":37,"faq":54,"tags":55},"mycobacterium-tuberculosis-lab-diagnosis","Laboratory Diagnosis of Mycobacterium tuberculosis Infection","Nisha Rijal","2020-05-26","2026-07-19",[],[46],{"slug":57,"title":58,"description":59,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":60,"lastUpdatedDate":61,"draft":41,"category":62,"image":37,"faq":63,"tags":64},"preparation-uses-lowenstein-jensen-lj-medium","Löwenstein-Jensen (LJ) Medium: Principle, Preparation, Uses, and Colony Characteristics","Löwenstein-Jensen (LJ) medium is the standard solid culture medium for Mycobacterium tuberculosis. Learn its principle, preparation by inspissation, colony characteristics of M. tuberculosis and NTM, and how LJ compares to MGIT liquid culture.","2016-04-29","2026-07-05","culture-media",[],[46],{"slug":66,"title":67,"description":68,"seoTitle":69,"seoDescription":37,"author":38,"createdDate":70,"lastUpdatedDate":71,"draft":41,"category":42,"image":37,"faq":72,"tags":109},"genexpert-mtbrif-assay-principle-procedure-results-interpretations","GeneXpert MTB\u002FRIF: How to Read the Result and What to Do Next","Semi-quantitative grades, probe-level RIF calls, error codes, and the traps: why a \"RIF resistance detected\" result still needs confirmation and why \"not detected\" never rules out TB.","GeneXpert MTB\u002FRIF Assay: Principle, Procedure, Results, and Interpretation","2016-01-04","2026-07-25",[73,76,79,82,85,88,91,94,97,100,103,106],{"question":74,"answer":75},"Does GeneXpert detect isoniazid resistance?","No. The assay reads only the rpoB gene and reports rifampicin resistance. Isoniazid resistance requires a line probe assay, targeted sequencing, or phenotypic DST. Because rifampicin resistance usually co-exists with isoniazid resistance, a positive RIF result is used as a marker for probable MDR-TB, but it is an inference, not a measurement.",{"question":77,"answer":78},"Can GeneXpert replace sputum smear microscopy and culture?","It replaces smear microscopy as the initial diagnostic test under current WHO guidance. It does not replace culture. Culture is still needed for phenotypic drug susceptibility testing, genotyping, detection of non-tuberculous mycobacteria, and confirmation of cure.",{"question":80,"answer":81},"What does \"MTB detected, trace\" mean?","It means the multicopy IS6110 or IS1081 targets were detected but rpoB was essentially unread, so bacillary load is at the very bottom of the assay's range and rifampicin resistance cannot be reported. In children, people living with HIV, and extrapulmonary specimens, trace counts as bacteriological confirmation of TB. In previously treated adults it should be repeated on a fresh specimen, because it may represent residual DNA from cured disease.",{"question":83,"answer":84},"Why does the report say \"very low\" or \"high\"?","That is the semi-quantitative grade, derived from the cycle threshold of the first rpoB probe to bind. It estimates bacillary load, which relates to infectiousness, to how reliable the rifampicin call is, and to the likelihood that a weak positive represents old rather than active disease.",{"question":86,"answer":87},"What is the difference between Invalid and Error?","Invalid means the Sample Processing Control failed: something about the specimen, usually inhibitors or inadequate processing, prevented a trustworthy result. Repeat with a new specimen. Error means the run aborted on an instrument or cartridge fault, most often a failed probe check or a pressure problem. Repeat with a new cartridge.",{"question":89,"answer":90},"Can a GeneXpert result be falsely positive for rifampicin resistance?","Yes. The assay infers resistance from a probe failing to bind, not from reading the mutation, so silent mutations and non-resistance-conferring polymorphisms in the RRDR are reported as resistance. False positives are most common on paucibacillary specimens. This is why a positive result should be confirmed by a line probe assay, targeted sequencing, or phenotypic DST, while treatment is started in parallel.",{"question":92,"answer":93},"Can GeneXpert miss rifampicin resistance?","Yes. Approximately 5% of rifampicin-resistant strains carry mutations outside the 81-bp RRDR. These leave all probes binding normally and are reported as susceptible.",{"question":95,"answer":96},"How long does the GeneXpert MTB\u002FRIF test take?","Under two hours from loading. The standard Xpert MTB\u002FRIF run is about 112 minutes; Xpert Ultra is faster at roughly 65 to 87 minutes. Specimen preparation adds about 15 to 20 minutes before loading.",{"question":98,"answer":99},"Can GeneXpert be used on non-sputum specimens?","Yes. WHO endorses its use on CSF, lymph node aspirate and tissue, gastric aspirate, nasopharyngeal aspirate, and stool, with sensitivity varying by specimen type. It is strongly recommended as the initial test in suspected TB meningitis. Sensitivity is lowest in pleural fluid.",{"question":101,"answer":102},"Can GeneXpert be used to monitor response to treatment?","No. It detects DNA from both living and dead bacilli, so it can remain positive for months in patients who are responding well. Smear microscopy and culture are used for treatment monitoring.",{"question":104,"answer":105},"Does a positive GeneXpert distinguish M. tuberculosis from M. bovis?","No. It detects the M. tuberculosis complex as a group and cannot separate M. tuberculosis, M. bovis, M. africanum, or BCG. Species-level identification requires culture-based methods.",{"question":107,"answer":108},"Is a biological safety cabinet required to run GeneXpert?","Specimen manipulation before the 15-minute inactivation step should be done in a Class II BSC where available. After that step the cartridge is closed and the risk is minimal. WHO permits Xpert testing at the same biosafety level as direct sputum smear microscopy in settings without a BSC.",[46],{"slug":111,"title":112,"description":113,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":114,"lastUpdatedDate":53,"draft":41,"category":115,"image":37,"faq":116,"tags":126},"auramine-rhodamine-fluorochrome-staining-principle-procedure-results-limitations","Auramine-Rhodamine Fluorochrome Staining: Principle, Procedure, and Results","Auramine-rhodamine is a WHO-recommended fluorochrome stain for detecting acid-fast bacilli — more sensitive than Ziehl-Neelsen and faster to screen. Learn the Truant method procedure, results grading, and when to confirm with ZN staining.","2015-04-03","staining-techniques",[117,120,123],{"question":118,"answer":119},"Why is auramine-rhodamine staining more sensitive than Ziehl-Neelsen for detecting acid-fast bacilli?","Auramine-rhodamine allows smear screening at 250x or 400x magnification — compared to 1,000x oil immersion required for ZN staining. At lower magnification, a much larger area of the slide can be examined per unit time (3-5 minutes vs 15-20 minutes per slide). This means more of the smear is examined, increasing the chance of detecting paucibacillary specimens. Studies consistently show auramine-rhodamine detects approximately 10% more positive cases than ZN in direct smear microscopy, which is why WHO recommends it as the preferred method where fluorescence microscopy is available.",{"question":121,"answer":122},"What is the two-step workflow for auramine-rhodamine results?","Positive auramine-rhodamine results should be confirmed by ZN staining of the same slide, as fluorescence artefacts (dust, fibres, non-AFB structures) can occasionally give false-positive fluorescence. Negative auramine-rhodamine results require examination of the minimum required number of fields before reporting — at 200-250x this is typically 30-100 fields. In high-suspicion patients, a negative fluorochrome result should prompt ZN confirmation and repeat specimen collection, as the minimum detection threshold for smear microscopy (approximately 5,000-10,000 AFB\u002FmL) means culture is more sensitive than any smear method.",{"question":124,"answer":125},"Can auramine-rhodamine staining detect organisms other than mycobacteria?","Yes. A modified fluorochrome method using a weaker decolouriser (0.5% sulphuric acid instead of 3% acid-alcohol) detects partially acid-fast organisms including Cryptosporidium parvum, Cyclospora cayetanensis, and Isospora belli oocysts in stool specimens, and Nocardia species in respiratory or wound specimens. These organisms share a partial acid-fast property with mycobacteria. The oocysts appear as bright yellow-orange fluorescent structures against a dark background. This application requires the modified decolouriser — the standard 3% acid-alcohol used for TB smears will over-decolourise these weakly acid-fast organisms.",[46],{"slug":128,"title":129,"description":129,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":130,"lastUpdatedDate":40,"draft":41,"category":42,"image":37,"faq":131,"tags":132},"short-notes-atypical-mycobacterial-infections","Atypical Mycobacterial Infections","2014-11-07",[],[46],{"slug":134,"title":135,"description":136,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":137,"lastUpdatedDate":138,"draft":41,"category":115,"image":37,"faq":139,"tags":149},"ziehl-neelsen-technique-principle-procedure-reporting","Ziehl-Neelsen Staining: Principle, Procedure, Grading, and Interpretation","The hot ZN acid-fast staining method step by step, why mycolic acid holds carbol fuchsin against acid-alcohol, WHO smear grading from scanty to 3+, and what a negative smear does and does not rule out in TB.","2013-12-06","2026-07-22",[140,143,146],{"question":141,"answer":142},"Why does Ziehl-Neelsen staining require heat while other staining techniques do not?","Mycobacteria have a cell wall rich in mycolic acids — long-chain fatty acids that make the wall waxy, hydrophobic, and impermeable to most dyes at room temperature. Heat acts as a mordant by disrupting this waxy barrier and allowing carbol fuchsin to penetrate the cell wall. Once inside, the stain is held so tightly by the mycolic acids that even acid-alcohol — one of the strongest decolorisers used in microbiology — cannot remove it. This is why the stain is called 'acid-fast' — the organisms hold fast to the dye even after acid treatment.",{"question":144,"answer":145},"How is an AFB smear graded and what does the grade mean clinically?","AFB smears are graded using the WHO\u002FIUATLD scale: No AFB seen (after examining 300 fields); Scanty — 1-9 AFB per 100 fields (report exact count and request repeat); 1+ — 10-99 AFB per 100 fields; 2+ — 1-10 AFB per field in at least 50 fields; 3+ — more than 10 AFB per field in at least 20 fields. Higher grades indicate greater organism burden and greater infectiousness. Grade is recorded at treatment initiation and at months 2, 5, and 6 to monitor bacteriological response. Conversion from positive to negative smear during treatment indicates therapeutic response.",{"question":147,"answer":148},"What is the difference between Ziehl-Neelsen and Kinyoun (cold) acid-fast staining?","Both methods use carbolfuchsin as the primary stain and acid-alcohol for decolourisation, but they differ in how the dye penetrates the mycobacterial cell wall. Ziehl-Neelsen uses heat (the hot technique) — the slide is steamed to drive the dye through the waxy cell wall. Kinyoun's cold technique achieves penetration without heat by increasing the concentration of both carbolfuchsin and phenol and incorporating a wetting agent (Triton X-100 or similar). The results are equivalent. Kinyoun is preferred where open flames are unsafe or inconvenient, and for partial acid-fast organisms (Nocardia, Cryptosporidium) where lower decoloriser concentrations are needed.",[46],{"slug":151,"title":152,"description":152,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":153,"lastUpdatedDate":40,"draft":41,"category":154,"image":37,"faq":155,"tags":156},"key-biochemical-methods-used-to-distinguish-mycobacterial-group","Biochemical Tests to identify Mycobacteria, NTM","2013-07-22","biochemical-tests",[],[46],{"slug":158,"title":159,"description":160,"seoTitle":37,"seoDescription":37,"author":51,"createdDate":161,"lastUpdatedDate":53,"draft":41,"category":42,"image":162,"faq":163,"tags":164},"tuberculin-skin-test-mantoux-test-principle-procedure-results","Tuberculin Skin Test (Mantoux test): Principle, Procedure, Results","Details about Tuberculin Skin Test.","2023-02-02","https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FMantoux_tuberculin_skin_test-1.jpg",[],[46],[166,172,179,184,188,192,197,202,206,210],{"slug":167,"name":38,"description":168,"image":169,"body":170,"postCount":171},"acharya-tankeshwar","Editor-in-chief","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Ftankeshwar-acharya-author-microbeonline.jpg","***Tankeshwar Acharya, MSc (Medical Microbiology)***\n\n*Tankeshwar Acharya is an Assistant Professor in the Department of Microbiology at Patan Academy of Health Sciences (PAHS), Nepal, where he has been teaching and practicing clinical microbiology for over 14 years. He is the founder of Microbe Online, one of the leading free microbiology education resources on the web, covering bacteriology, mycology, parasitology, immunology, and clinical laboratory diagnostics written from direct experience in both the classroom and the diagnostic laboratory.*",432,{"slug":173,"name":174,"description":175,"image":176,"body":177,"postCount":178},"ashma-shrestha","Ashma Shrestha","SEO Copywriter and Science Communicator\nKathmandu, Nepal","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fashma-shrestha.png","Ashma Shrestha holds a Master of Science in Medical Microbiology from the Institute of Science and Technology (IOST), Tribhuvan University, Nepal, where she developed a strong foundation in virology, molecular biology, and diagnostic microbiology.\n\nShe now works as an SEO Copywriter at Resolution Digital, where she combines her scientific training with research-driven content strategy. She is certified in Google Analytics and Google Business Profile (GBP), and brings a data-informed approach to science communication writing content that is not only accurate but structured to reach and serve the students who need it most.\n\nAt microbeonline, Ashma contributes articles primarily in virology and molecular biology, areas she finds most compelling for their mechanistic depth and their growing clinical relevance. Her writing reflects the same standard the site is built on: factual rigor, clear explanation of the *why* behind microbiology concepts, and content that helps students move from memorization to genuine understanding.\n\nShe is passionate about making complex microbiological concepts accessible without sacrificing accuracy; a skill that sits at the intersection of her scientific training and her professional work in content and SEO.",81,{"slug":180,"name":181,"description":182,"image":37,"body":37,"postCount":183},"sushmita-baniya","Sushmita Baniya","Author \u002F Contributor",32,{"slug":185,"name":186,"description":182,"image":37,"body":37,"postCount":187},"samikshya-acharya","Samikshya Acharya",20,{"slug":189,"name":190,"description":182,"image":37,"body":37,"postCount":191},"alisha-tripathi","Alisha Tripathi",6,{"slug":193,"name":194,"description":195,"image":37,"body":37,"postCount":196},"aastha-shrestha","Aastha Shrestha"," Author \u002F Contributor",10,{"slug":198,"name":199,"description":200,"image":37,"body":37,"postCount":201},"guest-author","Guest Author","Guest Author \u002F Contributor",2,{"slug":203,"name":204,"description":182,"image":37,"body":37,"postCount":205},"srijana-khanal","Srijana Khanal",18,{"slug":207,"name":208,"description":200,"image":37,"body":37,"postCount":209},"dr-poonam-acharya","Dr. Poonam Acharya",1,{"slug":211,"name":51,"description":182,"image":37,"body":212,"postCount":213},"nisha-rijal","**Nisha Rijal** is a microbiologist and quality assurance specialist. She served for nearly 12 years as a microbiologist at the National Public Health Laboratory (NPHL), Nepal's national reference laboratory, and continues to work as a consultant microbiologist in international public health organization. ",51]