Mycobacterium Tuberculosis
Dr. Suprakash Das
Asist. Prof.
History of Tuberculosis
 Tuberculosis is one of the oldest of humankind’s plagues.
 Mycobacterium tuberculosis probably emerged as a pathogen of our early
ancestors 20,000 to 15,000 years ago in east Africa.
 As humans peopled the globe, they took their diseases with them, including
tuberculosis.
 The writings of classical Greek and Roman physicians make it clear that they
recognized tuberculosis.
 During the 17th and 18th centuries, tuberculosis exploded with soaring prevalence.
 In 1680 John Bunyan described it as “the Captain among these men of death”.
 During the next 200 years this sobriquet would hold, as tuberculosis became a
leading cause of death in Europe and North America.
 A unified concept of tuberculosis first emerged with the work of Lae¨nnec in the
early 19th century.
Mycobacteria- Basic Bacteriology
 Mycobacteria belong to the family Mycobacteriaceae and the order
Actinomycetales.
 The organisms that belong to the genus Mycobacterium are
Aerobic (although some may grow in reduced oxygen concentrations),
Non–spore forming (except for Mycobacterium marinum),
Nonmotile,
Very thin, slightly curved or straight rods (0.2-0.6 3 1-10 𝛍m).
 Some species may display a branching morphology.
 Mycobacterium is the only genus in the Mycobacteriaceae family.
Mycobacteria- Basic Bacteriology
 Mycobacterium spp. have an unusual cell wall structure.
 The cell wall contains N-glycolylmuramic acid instead of N-acetylmuramic acid,
and it has a very high lipid content, which creates a hydrophobic permeability
barrier.
 Because of this cell wall structure, mycobacteria are difficult to stain with
commonly used basic aniline dyes, such as those used in Gram staining.
 Although these organisms cannot be readily Gram stained, they generally are
considered gram positive.
 However, they resist decolorization with acidified alcohol (3% hydrochloric
acid) after prolonged application of a basic fuchsin dye or with heating of this
dye after its application.
 This important property of mycobacteria, which derives from their cell wall
structure, is referred to as acid fastness; this characteristic distinguishes
mycobacteria from other genera.
Mycobacteria- Basic Bacteriology
 Another important feature of many species is that they grow more slowly than most
other human pathogenic bacteria because of their hydrophobic cell surface.
 Because of this hydrophobicity, organisms tend to clump, so that nutrients are not easily
allowed into the cell.
 A single cell’s generation time (the time required for a cell to divide into two
independent cells) may range from approximately 20 hours to 36 hours for
Mycobacterium ulcerans.
 Slow-growing mycobacteria, by definition, require more than 7 days to produce
colonies on solid media.
 The variation in generation times among the mycobacteria results in the formation of
visible colonies in 2 to 60 days at optimum temperature.
 Rapid-growing mycobacteria (RGMs), in which growth is apparent sooner than 7
days after subculture to Lowenstein-Jensen medium, may partially or completely lose
this characteristic as a result of their growth characteristics.
Mycobacterium Tuberculosis Complex and NTMs
 Mycobacteria can be divided into two major groups, based on fundamental
differences in epidemiology and association with disease: those belonging to the
M. tuberculosis complex and the NTM group.
 Currently, the genus Mycobacterium includes more than 150 recognized or
proposed species that are predominantly classified as nontuberculous
environmental mycobacteria (NTM).
 There are several species that are prominent pathogens, most notably the
Mycobacterium tuberculosis complex, Mycobacterium leprae, and Mycobacterium
ulcerans.
 In the clinical microbiology laboratory, the term complex is commonly used to
describe two or more species for which distinction is complicated and has little or
no medical importance.
Mycobacterium Tuberculosis Complex and NTMs
The mycobacterial species that belong to the M. tuberculosis complex
M. tuberculosis,
Mycobacterium bovis
Mycobacterium bovis BCG,
Mycobacterium africanum,
Mycobacterium caprae,
Mycobacterium microti,
Mycobacterium canettii,
Mycobacterium mungi,
Mycobacterium orygis,
Mycobacterium pinnipedii.
Mycobacterium Tuberculosis Complex and NTMs
All of these species are capable of causing tuberculosis.
It should be noted that species identification might be required for
epidemiologic and public health reasons.
The organisms that belong to the M. tuberculosis complex are
considered slow growers, and colonies are nonpigmented.
Cell wall of
M. tuberculosis
Epidemiology
 More than 5 million new cases of tuberculosis (all forms, both pulmonary
and extrapulmonary) were reported to the World Health Organization
(WHO) in 2005;
 >90% of cases were reported from developing countries.
 The WHO estimated that 8.8 million new cases of tuberculosis occurred
worldwide in 2005,
 95% of them in developing countries of Asia (4.9 million), Africa (2.6
million), the Middle East (0.6 million), and Latin America (0.4 million).
 It is further estimated that 1.6 million deaths from tuberculosis occurred in
2005, 95% of them in developing countries.
 An estimated 1.7 billion people, or one third of the world’s population, are
infected with M. tuberculosis.
Epidemiology
 This reservoir of infected individuals results in 8 million new cases of
tuberculosis and 2.9 million deaths annually.
 Tuberculosis continues to be a public health problem in the United States.
 An additional complicating factor in the management of tuberculosis is the
increasing incidence of coinfection with the human immunodeficiency virus
(HIV).
 HIV-associated tuberculosis remains a significant challenge to world health,
with an estimated 1.1 million individuals living with HIV-associated
tuberculosis.
 In the United States, tuberculosis typically is found among the poor, the
homeless, intravenous (IV) drug users, alcoholics, the elderly, or medically
underserved populations.
World map of countries by tuberculosis (TB) incidence
FROM EXPOSURE TO INFECTION
 M. tuberculosis is most commonly transmitted from a person with infectious pulmonary
tuberculosis to others by droplet nuclei, which are aerosolized by coughing, sneezing, or
speaking.
 The tiny droplets dry rapidly; the smallest (<5–10 μm in diameter) may remain suspended
in the air for several hours and may reach the terminal air passages when inhaled.
 There may be as many as 3000 infectious nuclei per cough.
 Other routes of transmission of tubercle bacilli (e.g., through the skin or the placenta) are
uncommon and of no epidemiologic significance.
Determinants of the likelihood of transmission
The probability of contact with a person who has an infectious form of tuberculosis,
The intimacy and duration of that contact,
The degree of infectiousness of the case, and
The shared environment in which the contact takes place are all important
FROM EXPOSURE TO INFECTION
 Tuberculosis patients whose sputum contains AFB visible by microscopy are the most
likely to transmit the infection.
 The most infectious patients have cavitary pulmonary disease or, much less commonly,
laryngeal tuberculosis and produce sputum containing as many as 105–107 AFB/mL.
 Patients with sputum smear–negative/culture-positive tuberculosis are less infectious,
and those with culture-negative pulmonary disease and extrapulmonary tuberculosis are
essentially non-infectious.
 Because persons with both HIV infection and tuberculosis are less likely to have
cavitations, they may be less infectious than persons without HIV co-infection.
 Crowding in poorly ventilated rooms is one of the most important factors in the
transmission of tubercle bacilli, since it increases the intensity of contact with a case.
 It is estimated that, in high-prevalence settings, up to 20 contacts may be infected by
each AFB-positive case before the index case is found to have tuberculosis.
FROM INFECTION TO DISEASE
 The risk of developing disease after being infected depends largely on endogenous
factors, such as
Individual’s innate immunologic defenses
Nonimmunologic defenses
Level of function of cell-mediated immunity (CMI).
 Clinical illness directly after infection is classified as primary tuberculosis and is
common among children up to 4 years of age and among
immunocompromised persons.
 Although primary tuberculosis may be severe and disseminated, it is not generally
associated with high-level transmissibility.
 When infection is acquired later in life, the chance is greater that the mature
immune system will contain it at least temporarily.
FROM INFECTION TO DISEASE
 The majority of infected individuals who ultimately develop tuberculosis do
so within the first year or two after infection.
 Dormant bacilli, however, may persist for years before reactivating to
produce secondary (or post-primary) tuberculosis, which, because of
frequent cavitation, is more often infectious than is primary disease.
 Overall, it is estimated that up to 10% of infected persons will eventually
develop active tuberculosis in their lifetime.
 The risk is much higher among HIV-infected persons.
 Reinfection of a previously infected individual, which is common in areas
with high rates of tuberculosis transmission, may also favor the
development of disease.
PATHOGENESIS-
INFECTION AND MACROPHAGE INVASION
 The interaction of M. tuberculosis with the human host begins when droplet nuclei
containing microorganisms from infectious patients are inhaled.
 Although the majority of inhaled bacilli are trapped in the upper airways and
expelled by ciliated mucosal cells, a fraction (usually <10%) reach the alveoli.
 There, alveolar macrophages that have not yet been activated phagocytize the
bacilli.
 Invasion of macrophages by mycobacteria results largely from binding of the
bacterial cell wall with a variety of macrophage cell-surface molecules,
including
Complement receptors,
Mannose receptor,
Immunoglobulin GFcγ receptor, and
Type A scavenger receptors
PATHOGENESIS-
INFECTION AND MACROPHAGE INVASION
 Phagocytosis is enhanced by complement activation leading to opsonization
of bacilli with C3 activation products such as C3b.
 After a phagosome forms, the survival of M. tuberculosis within it seems to
depend on reduced acidification due to lack of accumulation of vesicular
proton-adenosine triphosphatase.
 A complex series of events is probably generated by the bacterial cell-wall
glycolipid lipoarabinomannan (LAM).
 LAM inhibits the intracellular increase of Ca2+.Thus the
Ca2+/calmodulin pathway (leading to phagosome-lysosome fusion) is
impaired, and the bacilli may survive within the phagosomes.
 If the bacilli are successful in arresting phagosome maturation, then
replication begins and the macrophage eventually ruptures and releases its
bacillary contents.
Virulence Factors of
M. tuberculosis
INNATE RESISTANCE TO INFECTION
 The existence of this resistance, which is polygenic in nature, is suggested by the differing
degrees of susceptibility to tuberculosis in different population.
 The human gene NRAMP1 (natural resistance–associated macrophage protein 1), which maps
to chromosome 2q, may play a role in determining susceptibility to tuberculosis.
 Polymorphisms in multiple genes, such as those encoding for
Histocompatibility leukocyte antigen (HLA),
Interferon γ (IFN-γ),
T-cell growth factor β (TGF-β),
Interleukin (IL) 10,
Mannose-binding protein,
IFN-γ receptor,
Toll-like receptor (TLR) 2,
Vitamin D receptor, and IL-1, have been associated with susceptibility to tuberculosis.
THE HOST RESPONSE
 In the initial stage of host-bacterium interaction, either fusion between
phagosomes and lysosomes occurs, preventing bacillary survival, or the
bacilli begin to multiply, ultimately killing the macrophage.
A variety of chemo-attractants that are released after cell lysis
Complement components
Bacterial molecules
Cytokines Recruit additional immature monocyte-derived macrophages,
including dendritic cells, which migrate to the draining lymph nodes and
present mycobacterial antigens to T lymphocytes.
 At this point, the development of CMI and humoral immunity begins.
 These initial stages of infection are usually asymptomatic.
THE HOST RESPONSE
 About 2–4 weeks after infection, two host responses to M. tuberculosis develop:
Macrophage-activating CMI response
Tissue-damaging response.
 The macrophage activating response is a T-cell–mediated phenomenon
resulting in the activation of macrophages that are capable of killing and
digesting tubercle bacilli.
 The tissue-damaging response is the result of a delayed-type hypersensitivity
(DTH) reaction to various bacillary antigens.
 It destroys inactivated macrophages that contain multiplying bacilli but also
causes caseous necrosis of the involved tissues.
 Both of these responses can inhibit mycobacterial growth,
 It is the balance between the two that determines the form of tuberculosis
that will develop subsequently.
GRANULOMA FORMATION
 With the development of specific immunity and the accumulation of large
numbers of activated macrophages at the site of the primary lesion,
granulomatous lesions (tubercles) are formed.
 These lesions consist of accumulations of lymphocytes and activated
macrophages that evolve toward epithelioid and giant cell morphologies.
 Initially, the tissue-damaging response can limit mycobacterial growth within
macrophages.
 As stated above, this response, mediated by various bacterial products, not only
destroys macrophages but also produces early solid necrosis in the center of the
tubercle.
 Although M. tuberculosis can survive, its growth is inhibited within this necrotic
environment by low oxygen tension and low pH.
 At this point, some lesions may heal by fibrosis, with subsequent calcification,
whereas inflammation and necrosis occur in other lesions.
THE MACROPHAGE-ACTIVATING RESPONSE
 CMI is critical at this early stage.
 In the majority of infected individuals, local macrophages are activated when
bacillary antigens processed by macrophages stimulate T lymphocytes to release a
variety of lymphokines.
 These activated macrophages aggregate around the lesion’s center and effectively
neutralize tubercle bacilli without causing further tissue destruction.
 In the central part of the lesion, the necrotic material resembles soft cheese
(caseous necrosis)—a phenomenon that may also be observed in other conditions,
such as neoplasms.
 Even when healing takes place, viable bacilli may remain dormant within
macrophages or in the necrotic material for many years.
 These “healed” lesions in the lung parenchyma and hilar lymph nodes may later
undergo calcification.
THE DELAYED-TYPE
HYPERSENSITIVITY REACTION
 In a minority of cases, the macrophage-activating response is weak, and mycobacterial growth
can be inhibited only by intensified DTH reactions, which lead to lung tissue destruction.
 The lesion tends to enlarge further, and the surrounding tissue is progressively damaged.
 At the center of the lesion, the caseous material liquefies.
 Bronchial walls as well as blood vessels are invaded and destroyed, and cavities are formed.
 The liquefied caseous material, containing large numbers of bacilli, is drained through bronchi.
 Within the cavity, tubercle bacilli multiply, spill into the airways, and are discharged into
the environment through expiratory maneuvers such as coughing and talking.
 In the early stages of infection, bacilli are usually transported by macrophages to regional lymph
nodes, from which they gain access to the bloodstream and disseminate widely throughout the
body.
 In young children with poor natural immunity, hematogenous dissemination may result in
fatal miliary tuberculosis or tuberculous meningitis.
Stages of granuloma
formation during tuberculosis.
 Initial phase of Mycobacterium tuberculosis infection leads to induction of
innate responses and apoptosis.
 The consequential chemotactic signals help recruiting more of uninfected
macrophages to the site of infection.
 Some of the infected macrophages also egress and seed new granulomas.
 The advent of adaptive immunity results in attainment of equilibrium
between the pathogen and host immune system.
 The overall bacterial load keeps on increasing during granuloma maturation
till equilibrium is attained.
 When a person is immunocompromised, caseation occurs and rapid
bacillary dissemination takes place.
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 Tuberculosis is classified as pulmonary, extrapulmonary, or both.
 Before the advent of HIV infection, ∼80% of all new cases of tuberculosis were limited to
the lungs.
 However, up to two-thirds of HIV-infected patients with tuberculosis may have both
pulmonary and extrapulmonary disease or extrapulmonary disease alone.
 Pulmonary tuberculosis can be categorized as primary or postprimary (secondary).
Primary Disease
 Primary pulmonary tuberculosis occurs soon after the initial infection with tubercle
bacilli, often seen in children.
 Because most inspired air is distributed to the middle and lower lung zones, these areas of
the lungs are most commonly involved in primary tuberculosis.
 The lesion forming after infection is usually peripheral and accompanied in more than
half of cases by hilar or paratracheal lymphadenopathy, which may not be detectable
on chest radiography.
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 In the majority of cases, the lesion heals spontaneously and may later be evident as a
small calcified nodule (Ghon lesion).
 In children and in persons with impaired immunity (e.g., those with malnutrition or HIV
infection), primary pulmonary tuberculosis may progress rapidly to clinical illness.
 The initial lesion increases in size and can evolve in different ways.
 Pleural effusion (two-thirds of cases) results from the penetration of bacilli into the
pleural space from an adjacent subpleural focus.
 In severe cases, the primary site rapidly enlarges, its central portion undergoes necrosis,
and cavitation develops (Progressive primary tuberculosis).
 Tuberculosis in young children is almost invariably accompanied by hilar or mediastinal
lymphadenopathy due to the spread of bacilli from the lung parenchyma through
lymphatic vessels.
 Enlarged lymph nodes may compress bronchi, causing obstruction and subsequent
segmental or lobar collapse.
Ghon lesion
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 Partial obstruction may cause obstructive emphysema, and
bronchiectasis may also develop.
 Hematogenous dissemination, which is common and often
asymptomatic, may result in the most severe manifestations of primary
M. tuberculosis infection.
 Bacilli reach the bloodstream from the pulmonary lesion or the lymph
nodes and disseminate into various organs, where they may produce
granulomatous lesions.
 Although healing frequently takes place, immunocompromised
persons (e.g., patients with HIV infection) may develop miliary
tuberculosis and/or tuberculous meningitis.
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
Postprimary Disease
 Also called adult-type, reactivation, or secondary tuberculosis, postprimary disease
results from endogenous reactivation of latent infection.
 Usually localized to the apical and posterior segments of the upper lobes, where the
substantially higher mean oxygen tension (compared with that in the lower zones)
favors mycobacterial growth. The superior segments of the lower lobes are frequently
involved.
 The extent of lung parenchymal involvement varies greatly, from small infiltrates to
extensive cavitary disease.
 With cavity formation, liquefied necrotic contents are ultimately discharged into the
airways, resulting in satellite lesions within the lungs that may in turn undergo
cavitation.
 Massive involvement of pulmonary segments or lobes, with coalescence of lesions,
produces Tuberculous pneumonia.
Cavitary Pulmonary Lesions
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 Although up to one third of untreated patients reportedly succumb to severe
pulmonary tuberculosis within a few weeks or months after onset (the
classical “galloping consumption” of the past),
 Others undergo a process of spontaneous remission or proceed along a
chronic, progressively debilitating course (“consumption”).
 Under these circumstances, some pulmonary lesions become fibrotic and
may later calcify, but cavities persist in other parts of the lungs.
 Individuals with such chronic disease continue to discharge tubercle bacilli
into the environment.
 Most patients respond to treatment, with defervescence, decreasing cough,
weight gain, and a general improvement in well-being within several weeks.
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 Early in the course of disease, symptoms and signs are often nonspecific and
insidious, consisting mainly of fever and night sweats, weight loss, anorexia,
general malaise, and weakness.
 However, in the majority of cases, cough eventually develops—often initially
nonproductive and subsequently accompanied by the production of purulent
sputum, sometimes with blood streaking.
 Massive hemoptysis may ensue as a consequence of the erosion of a blood vessel
in the wall of a cavity.
 Hemoptysis, however, may also result from rupture of a dilated vessel in a cavity
(Rasmussen’s aneurysm) or from aspergilloma formation in an old cavity.
 Pleuritic chest pain sometimes develops in patients with subpleural parenchymal
lesions.
 Extensive disease may produce dyspnea and, in rare instances, adult respiratory
distress syndrome (ARDS).
CLINICAL MANIFESTATIONS-
Pulmonary Tuberculosis
 Physical findings are of limited use in pulmonary tuberculosis. Many patients have
no abnormalities detectable by chest examination, whereas
 Others have detectable rales in the involved areas during inspiration, especially
after coughing.
 Occasionally, rhonchi due to partial bronchial obstruction and classic amphoric
breath sounds in areas with large cavities may be heard.
 Systemic features include fever (often low-grade and intermittent) in up to
80% of cases and wasting.
 Absence of fever, however, does not exclude tuberculosis.
 In some cases, pallor and finger clubbing develop.
 The most common hematologic findings are mild anemia and leukocytosis.
 Hyponatremia due to the syndrome of inappropriate secretion of antidiuretic
hormone (SIADH) has also been reported.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Lymph-Node Tuberculosis (Tuberculous Lymphadenitis)
 The most common presentation of extrapulmonary tuberculosis, lymph-node disease
is particularly frequent among HIV-infected patients.
 In the United States, children and women (particularly non-Caucasians) also seem to be
especially susceptible.
 Once caused mainly by M. bovis, tuberculous lymphadenitis is today due largely to M.
tuberculosis.
 Lymph-node tuberculosis presents as painless swelling of the lymph nodes, most
commonly at posterior cervical and supraclavicular sites (a condition historically
referred to as Scrofula).
 Lymph nodes are usually discrete and nontender in early disease but may be inflamed and
have a fistulous tract draining caseous material.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Associated pulmonary disease is seen in >40% of cases.
 The diagnosis is established only by fine needle aspiration or surgical
biopsy.
 AFB are seen in up to 50% of cases, cultures are positive in 70–80%, and
histologic examination shows granulomatous lesions.
 Among HIV-infected patients, granulomas usually are not seen.
Differential diagnosis
Lymphomas or metastatic carcinomas, and rare disorders like
Kikuchi’s disease (necrotizing histiocytic lymphadenitis),
Kimura’s disease, and
Castleman’s disease.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Pleural Tuberculosis
 Involvement of the pleura, may result from
Contiguous spread of parenchymal inflammation,
Actual penetration by tubercle bacilli into the pleural space.
 Depending on the extent of reactivity, the effusion may be small, remain
unnoticed, and resolve spontaneously or may be sufficiently large to cause
symptoms such as fever, pleuritic chest pain, and dyspnea.
 Physical findings are those of pleural effusion: dullness to percussion and
absence of breath sounds.
 A chest radiograph reveals the effusion and, in up to one-third of cases, also shows
a parenchymal lesion.
 Thoracentesis is required to ascertain the nature of the effusion and to differentiate
it from manifestations of other etiologies.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
The fluid is
 Straw colored and at times hemorrhagic;
 It is an exudate with a protein concentration >50% of that in serum
(usually ∼4–6 g/dL),
 A normal to low glucose concentration,
 A pH of ∼7.3 (occasionally <7.2), and
 Detectable white blood cells (usually 500–6000/μL).
 Neutrophils may predominate in the early stage, whereas mononuclear
cells are the typical finding later.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Mesothelial cells are generally rare or absent.
 AFB are seen on direct smear in only 10–25% of cases, but cultures
may be positive for M. tuberculosis in 25–75% of cases;
 Positive cultures are more common among postprimary cases.
 Determination of the pleural concentration of adenosine deaminase
(ADA) is a useful screening test.
 Tuberculosis is virtually excluded if the value is very low.
 Needle biopsy of the pleura is often required for diagnosis and reveals
granulomas and/or yields a positive culture in up to 80% of cases.
TB Pleural Effusion
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Tuberculous empyema is a less common complication of pulmonary tuberculosis.
 It is usually the result of the rupture of a cavity, with spillage of a large number of
organisms into the pleural space.
 This process may create a bronchopleural fistula with evident air in the pleural space.
 A chest radiograph shows hydropneumothorax with an air-fluid level.
 The pleural fluid is purulent and thick and contains large numbers of lymphocytes.
 Acid-fast smears and mycobacterial cultures are often positive.
 Surgical drainage is usually required as an adjunct to chemotherapy.
 Tuberculous empyema may result in severe pleural fibrosis and restrictive lung
disease.
 Removal of the thickened visceral pleura (decortication) is occasionally necessary to
improve lung function.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Tuberculosis of the Upper Airways Nearly always a complication of advanced cavitary
pulmonary tuberculosis, tuberculosis of the upper airways may involve the larynx,
pharynx, and epiglottis.
Symptoms include
Hoarseness,
Dysphonia, and
Dysphagia
Chronic productive cough.
 Findings depend on the site of involvement, and ulcerations may be seen on
laryngoscopy.
 Acid-fast smear of the sputum is often positive, but biopsy may be necessary in some
cases to establish the diagnosis.
 Carcinoma of the larynx may have similar features but is usually painless.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Genitourinary tuberculosis, which accounts for ∼15% of all extrapulmonary cases
in the United States, may involve any portion of the genitourinary tract.
Urinary frequency,
Dysuria,
Nocturia,
Hematuria, and
Flank or abdominal pain are common presentations.
 Urinalysis gives abnormal results in 90% of cases, revealing pyuria and hematuria.
 The documentation of culture negative pyuria in acidic urine raises the suspicion
of tuberculosis.
 Intravenous pyelography, abdominal CT, or MRI may show deformities and
obstructions, and calcifications and ureteral strictures are suggestive findings.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Culture of three morning urine specimens yields a definitive diagnosis in nearly
90% of cases.
 Severe ureteral strictures may lead to hydronephrosis and renal damage.
 Genital tuberculosis is diagnosed more commonly in female than in male patients.
 In female patients, it affects the fallopian tubes and the endometrium and may
cause infertility, pelvic pain, and menstrual abnormalities.
 Diagnosis requires biopsy or culture of specimens obtained by dilatation and
curettage.
 In male patients, tuberculosis preferentially affects the epididymis, producing a
slightly tender mass that may drain externally through a fistulous tract;
 orchitis and prostatitis may also develop.
 In almost half of cases of genitourinary tuberculosis, urinary tract disease is also
present.
Renal TB
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Skeletal Tuberculosis
 In bone and joint disease, pathogenesis is related to reactivation of hematogenous
foci or to spread from adjacent paravertebral lymph nodes.
 Weight-bearing joints (the spine in 40% of cases, the hips in 13%, and the knees in
10%) are most commonly affected.
 Spinal tuberculosis (Pott’s disease or tuberculous spondylitis; often involves
two or more adjacent vertebral bodies.
 Although the upper thoracic spine is the most common site of spinal
tuberculosis in children, the lower thoracic and upper lumbar vertebrae are
usually affected in adults.
 From the anterior superior or inferior angle of the vertebral body, the lesion slowly
reaches the adjacent body, later affecting the intervertebral disk.
 With advanced disease, collapse of vertebral bodies results in kyphosis (gibbus).
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 A paravertebral “cold” abscess may also form.
 In the upper spine, this abscess may track to and penetrate the chest wall,
presenting as a soft tissue mass.
 In the lower spine, it may reach the inguinal ligaments or present as a psoas
abscess.
 CT or MRI reveals the characteristic lesion and suggests its etiology.
 The differential diagnosis includes tumors and Pyogenic bacterial
osteomyelitis.
 Aspiration of the abscess or bone biopsy confirms the tuberculous etiology,
as cultures are usually positive and histologic findings highly typical.
 A catastrophic complication of Pott’s disease is paraplegia, which is
usually due to an abscess or a lesion compressing the spinal cord.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Paraparesis due to a large abscess is a medical emergency and requires rapid
drainage.
 Tuberculosis of the hip joints, usually involving the head of the femur, causes
pain
 Tuberculosis of the knee produces pain and swelling.
 If the disease goes unrecognized, the joints may be destroyed.
 Diagnosis requires examination of the synovial fluid, which is
Thick in appearance,
High protein concentration and
Variable cell count.
 Synovial fluid culture is positive in a high percentage of cases,
 Synovial biopsy and tissue culture may be necessary to establish the diagnosis.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Tuberculous Meningitis and Tuberculoma
 It is seen most often in young children but also develops in adults, especially those
infected with HIV.
 Tuberculous meningitis results from the hematogenous spread of primary or
postprimary pulmonary disease or from the rupture of a subependymal tubercle
into the subarachnoid space.
 In more than half of cases, evidence of old pulmonary lesions or a miliary pattern
is found on chest radiography.
The disease often presents subtly as
 Headache and slight mental changes after a
 Prodrome of weeks of low-grade fever, malaise, anorexia, and irritability.
 If not recognized, tuberculous meningitis may evolve acutely with severe
headache, confusion, lethargy, altered sensorium, and neck rigidity.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Paresis of cranial nerves (ocular nerves in particular) is a frequent finding,
and the involvement of cerebral arteries may produce focal ischemia.
 The ultimate evolution is toward coma, with hydrocephalus and intracranial
hypertension. Lumbar puncture is the cornerstone of diagnosis.
Cerebrospinal fluid (CSF) examination reveals
High leukocyte count (up to 1000/μL), predominance of lymphocytes
Sometimes with a predominance of neutrophils in the early stage
Protein content of 1–8 g/L (100–800 mg/dL)
Low glucose concentration.
 However, any of these three parameters can be within the normal range.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 AFB are seen on direct smear of CSF sediment in up to one-third of cases, but
repeated lumbar punctures increase the yield.
 Culture of CSF is diagnostic in up to 80% of cases and remains the gold standard.
 Polymerase chain reaction (PCR) has a sensitivity of up to 80%, but rates of false-
positivity reach 10%.
 The ADA concentration may be a sensitive test but has low specificity.
 Imaging studies (CT and MRI) may show hydrocephalus and abnormal
enhancement of basal cisterns or ependyma.
 Tuberculoma, an uncommon manifestation of CNS tuberculosis, presents as one
or more space-occupying lesions and usually causes seizures and focal signs.
 CT or MRI reveals contrast-enhanced ring lesions, but biopsy is necessary to
establish the diagnosis.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Gastrointestinal Tuberculosis
 Various pathogenetic mechanisms are involved
Swallowing of sputum with direct seeding,
Hematogenous spread,
Ingestion of milk from cows affected by bovine tuberculosis.
 Terminal ileum and the cecum are the sites most commonly involved.
 Abdominal pain (at times similar to that associated with appendicitis) and
swelling,
 Obstruction,
 Hematochezia
 Palpable mass in the abdomen are common findings at presentation.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Fever,
 Weight loss,
 Anorexia, and
 Night sweats are also common.
 With intestinal-wall involvement, ulcerations and fistulae may simulate
Crohn’s disease; the differential diagnosis with this entity is always
difficult.
 Anal fistulae should prompt an evaluation for rectal tuberculosis.
 As surgery is required in most cases, the diagnosis can be established by
histologic examination and culture of specimens obtained intraoperatively.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Tuberculous peritonitis follows either
 Direct spread of tubercle bacilli from ruptured lymph nodes and intraabdominal organs (e.g.,
genital tuberculosis in women)
 Hematogenous seeding.
Nonspecific abdominal pain
Fever
Ascites
Paracentesis reveals
 Exudative fluid with a high protein content and
 Leukocytosis that is usually lymphocytic (although neutrophils occasionally predominate).
 The yield of direct smear and culture is relatively low.
 Peritoneal biopsy (with a specimen best obtained by laparoscopy) is often needed to establish the
diagnosis.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Pericardial Tuberculosis (Tuberculous Pericarditis)
Due to
Direct progression of a primary focus within the pericardium,
Reactivation of a latent focus, or
Rupture of an adjacent subcarinal lymph node,
 Pericardial tuberculosis has often been a disease of the elderly in countries with
low tuberculosis prevalence but also develops frequently in HIV-infected patients.
 Case-fatality rates are as high as 40% in some series.
 The onset may be subacute, although an acute presentation, with dyspnea, fever,
dull retrosternal pain, and a pericardial friction rub, is possible.
 An effusion eventually develops in many cases.
 Cardiovascular symptoms and signs of cardiac tamponade may ultimately appear.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 CT, or MRI shows effusion and thickness across the pericardial space.
 A definitive diagnosis can be obtained by pericardiocentesis under
echocardiographic guidance.
 The pericardial fluid must be submitted for biochemical, cytologic, and
microbiologic study.
 The effusion is exudative in nature, with a high count of leukocytes
(predominantly mononuclear cells).
 Hemorrhagic effusion is frequent.
 Direct smear examination is very rarely positive.
 Culture of pericardial fluid reveals M. tuberculosis in up to two thirds of
cases, whereas pericardial biopsy has a higher yield.
 High levels of ADA and IFN-γ may also suggest a tuberculous etiology.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Miliary or Disseminated Tuberculosis
 Miliary tuberculosis is due to hematogenous spread of tubercle bacilli.
 Consequence of primary infection/ reactivation of old disseminated foci.
 The lesions are usually yellowish granulomas 1–2 mm in diameter that resemble
millet seeds (thus the term miliary, coined by nineteenth-century pathologists).
 Fever, night sweats, anorexia, weakness, and weight loss are presenting
symptoms in the majority of cases.
 At times patients have a cough and other respiratory symptoms due to
pulmonary involvement, as well as abdominal symptoms.
 Physical findings include hepatomegaly, splenomegaly, and lymphadenopathy.
 Eye examination may reveal Choroidal tubercles, which are pathognomonic of
miliary tuberculosis, in up to 30% of cases.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Meningismus occurs in <10% of cases.
 A rare presentation seen in the elderly is cryptic military tuberculosis, which
has a chronic course characterized by
Mild intermittent fever
Anemia
Meningeal involvement preceding death.
 An acute septicemic form, Nonreactive miliary tuberculosis, occurs very
rarely and is due to massive hematogenous dissemination of tubercle bacilli.
 Pancytopenia is common in this form of disease, which is rapidly fatal.
 At postmortem examination, multiple necrotic but nongranulomatous
(“nonreactive”) lesions are detected.
Miliary tuberculosis
Miliary tuberculosis
Choroidal tubercles
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Less Common Extrapulmonary Forms
Ophthalmic Manifestations
 Chorioretinitis,
 Uveitis,
 Panophthalmitis, and
 Painful hypersensitivity-related phlyctenular conjunctivitis.
Tuberculous otitis
 Hearing loss,
 Otorrhea, and
 Tympanic membrane perforation.
 In the nasopharynx, tuberculosis may simulate Wegener’s granulomatosis.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
Cutaneous manifestations
Primary infection due to direct inoculation,
Abscesses and chronic ulcers,
Scrofuloderma,
Lupus vulgaris (a smoldering disease with nodules, plaques, and fissures),
Miliary lesions, and
Erythema nodosum.
 Adrenal tuberculosis is a manifestation of disseminated disease presenting rarely
as adrenal insufficiency.
 Finally, congenital tuberculosis results from transplacental spread of tubercle
bacilli to the fetus or from ingestion of contaminated amniotic fluid.
 This rare disease affects the liver, spleen, lymph nodes, and various other organs.
Scrofuloderma
Lupus vulgaris
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Tuberculosis can appear at any stage of HIV infection, and its presentation
varies with the stage.
 When CMI is only partially compromised, pulmonary tuberculosis presents
in a typical manner, with upper-lobe infiltrates and cavitation and without
significant lymphadenopathy or pleural effusion.
In late stages of HIV infection
Primary tuberculosis–like pattern,
Diffuse interstitial or miliary infiltrates,
Little or no cavitation,
Intrathoracic lymphadenopathy, is more common.
CLINICAL MANIFESTATIONS-
Extra Pulmonary Tuberculosis
 Overall, sputum smears may be positive less frequently among tuberculosis
patients with HIV infection than among those without.
 The diagnosis of tuberculosis may be unusually difficult, especially in view
of the variety of HIV-related pulmonary conditions mimicking tubercu
 Extrapulmonary tuberculosis—alone or in association with pulmonary
disease—has been documented in 40–60% of all cases in HIV–co-infected
individuals.
 The most common forms are lymphatic, disseminated, pleural, and
pericardial.
 Mycobacteremia and meningitis are also frequent, particularly in advanced
HIV disease.
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Laboratory Diagnosis
Direct Detection Methods Microscopy
 Sputum smear microscopy still remains the basis for diagnosis of TB in
developing countries.
 The most regular practice is acid-fast staining using carbol fuschin (Z-N stain)
and fluorochrome dye-auramine/rhodamine.
 It is relatively fast, inexpensive and specific for TB in high incidence areas.
 Although highly specific, smear microscopy is insensitive – it detects roughly
50% of all the active cases of TB (10,000 bacilli/ml need to be present).
 Sensitivity can be as low as 20% in children and HIV-infected people.
 As per the current Revised National Tuberculosis Control Programme (RNTCP)
guidelines, the patient should visit the clinic at least twice to submit a spot –
early morning or spot-spot specimen.
 At least two ml specimen should be collected which should be mucopurulent.
 Sputum specimens should be examined within two days of collection.
Laboratory Diagnosis
Direct Detection Methods Microscopy
 Routine microscopy cannot differentiate between live and dead bacilli and
hence cannot be used as a follow-up diagnostic test.
 It can neither be used to predict MDR nor the presence of non-tuberculous
mycobacteria.
 Despite the multitude of disadvantages, in the absence of better alternatives, it is a
useful tool in the basic laboratories common in developing countries.
 RNTCP has revised the diagnostic algorithm to allow for nucleic acid
amplification detection based on cartridge based technologies (CBNAAT) for
cases who are smear positive with presumptive MDR-TB/ or living in high MDR-
TB areas (>5% and >20% among new and retreatment cases respectively).
 It also allows simultaneous testing of second specimen by the above mentioned
cartridge based technology for smear negative cases with radiological
abnormalities and even those solely based on high clinical suspicion in spite of
negative CXR and smear.
Laboratory Diagnosis
Direct Detection Methods Microscopy
Fluorescent microscopy with light-emitting diodes
 Light-emitting diodes (LEDs) are more robust, sustainable and user-friendly, thus
allowing advantages of FM at peripheral health-care systems.
Advantages
Extremely long life expectancy.
Furthermore, they do not produce ultraviolet (UV) light
Do not require darkened rooms and
Significantly decrease the instrument’s power consumption
Longer lasting battery life.
 FM increases the sensitivity of smear microscopy as it allows a much larger area
of the smear to be seen, resulting in more rapid examination of the specimen (up
to four times faster).
Laboratory Diagnosis
Direct Detection Methods Microscopy
 RNTCP has adopted LED microscopy to replace ZN method in its designated microscopy
centres (DMCs) across India.
 Instability of fluorescent stains under field conditions and instability of the stained
smears for blinded rechecking have been reported.
Vital fluorescent staining
 Monitoring the response to TB treatment is essential for early detection of treatment
failure or drug resistance.
 Recent studies proposed a simple and instant method for TB treatment monitoring, based
on a common fluorescent viability marker, fluorescein diacetate (FDA), in combination
with smear microscopy.
 Unlike most fluorescent stains, FDA stains only living, cultivable bacteria thus guiding
antimicrobial therapy before culture reports come in.
Laboratory Diagnosis
Direct Detection Methods Microscopy
Newer microscopic technologies
 Automated microscopic technology by TBDx (Signature Mapping
Medical Sciences, USA) integrates robotic loading of stained slides and
automated high-resolution digital image analysis to provide a result in
minutes.
 The system has a 200-slide capacity reducing the burden on technicians.
 Early studies suggested improved sensitivity over the human eye, but
specificity was reduced;
 Manual review of positive slides was necessary.
 A second innovation to assist a microscopist is CellScope, a portable digital
FM that provides enlarged digitalised images for review
TBDx (Signature
Mapping Medical
Sciences, USA)
Laboratory Diagnosis
Direct Detection Methods Culture
 Culture still remains the gold standard for diagnosis of TB
 It permits the diagnosis of drug resistance, including the emerging mutations.
 Traditional egg-based (Lowenstein-Jensen) and agar-based (Middlebrook 7H10/11)
methods are widely used.
 The limit of detection is 100 bacilli/ml, thus increasing the sensitivity compared to
smear.
 the growth in a conventional egg-based medium takes anywhere from 4 to 8 weeks with
an additional 4 weeks for drug sensitivity by the conventional proportion method.
 Thus, it takes a median of 70 days to diagnose a case of MDR-TB by conventional
culture methods.
 Other limitations include requirement of biosafety facilities that are expensive to build
and maintain and specially trained laboratory technicians to perform the procedure.
 Hence, TB cultures are performed only at national reference laboratories
Laboratory Diagnosis
Direct Detection Methods Culture
 Mostly reserved for treatment failure and drug-resistant cases.
 Specimens often need to be sent to distant laboratories leading to delay in processing.
 Currently WHO/ RNTCP Recommend liquid culture using Middlebrook 7H9 broth
– Mycobacterial growth indicator tube (MGIT), a non-radiometric detection method
which measures the consumption of oxygen by fluorescence.
 As bacteria grow in the culture, the oxygen is utilised causing it to be fluorescent when
placed under UV light.
 Methods for testing for drug susceptibility follow the same principle but use two culture
samples:
One with a drug added
One without the drug (a growth control)
 It is called the Modified 1% proportion sensitivity testing method (PST).
Laboratory Diagnosis
Direct Detection Methods Culture
 In cases of rifampicin resistance (by CBNAAT Test), DST results of all the drugs
should be made available.
 If the test drug is active against the TB bacteria, it will inhibit growth and suppress
fluorescence.
 Automated systems have the capacity for up to 960 cultures at a time.
 Liquid culture systems provide results significantly faster
Diagnosis can be performed in 9 days for a smear-positive case
16 days for a smear-negative case.
Negative result is issued by 42 days.
DST takes an average 7–14 days after the initial culture.
 Automated systems can benefit laboratories with a high workload and provide
standardised reading of samples.
Laboratory Diagnosis
Direct Detection Methods Culture
 Such systems have a sensitivity and specificity of nearly 100%.
 Both automated and manual systems perform well in the detection of
INH and RIF susceptibility but are not as effective for ethambutol
(EMB) and streptomycin.
 Liquid media are more prone to contamination than solid media,
leading to invalid results unless carefully controlled.
 Internal quality control of culture involves testing of each batch for
sterility and quality strain H37Rv for growth parameters.
 For DST Sensitive strain (H37Rv) and mono-resistant strains
are tested batch wise.
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Laboratory Diagnosis
Direct Detection Rapid identification of species.
 Rapid speciation is necessary for the isolates grown in culture to differentiate between M.
tuberculosis (MTB) complex and other species of Mycobacteria.
 Conventional biochemical methods of speciation using para-nitrobenzoic acid can take
weeks.
 Strip speciation test can detect a TB-specific antigen (MPT 64) from positive liquid or
solid cultures to confirm the presence of organisms belonging to M. tuberculosis
complex.
 M. tuberculosis protein 64 (MPT-64) antigen is an M. tuberculosis complex (MTBC)-
specific antigen secreted during bacterial growth.
 This test provides results within 15 min and is highly sensitive and specific.
 Sensitivity and specificity were found to be 98.6% and 97.9%, respectively, for the
Capilia TB assay (Taunus, Japan).
 The intermediate reference laboratories (IRLs) in India utilize this antigen detection for
rapid identification of M. tuberculosis complex.
Laboratory Diagnosis
Direct Detection Antigen Detection
 Lipoarabinomannan (LAM) is a 17.5 kD glycolipid found in the outer cell
wall of mycobacterial species.
 It is immunogenic and a major virulence factor promoting survival in
human host.
 The test is available as an ELISA or dipstick method with a turnaround time
(TAT) of 4–6 h or 20 min depending on the test kit used.
 The WHO recommends that it should not be used for the diagnosis of TB,
except for
HIV-positive in-patients with signs and symptoms of TB (pulmonary
and/or extrapulmonary)
Who have a CD4 cell count ≤100 cells/μL or,
HIV-positive patients who are seriously ill, regardless of the CD4 count.
Laboratory Diagnosis
Direct Detection Antigen Detection
 For TB diagnosis among symptomatic patients, overall lateral
flow-LAM pooled sensitivity was 44% and pooled specificity was
92%.
 Higher sensitivity of urine LAM detection in patients with HIV
Higher bacillary burden and antigen load,
Greater likelihood of TB in the genitourinary tract and
Greater glomerular permeability that allows increased antigen levels
in urine.
Laboratory Diagnosis
Direct Detection Molecular detection:NAATs
 Most molecular methods that are WHO endorsed detect the nucleic acid
(DNA) of both live and dead bacilli.
 While molecular methods cannot as yet completely replace culture and
phenotypic DST, implementation of these assays
Reduces the need for costly laboratory infrastructure and
Detect MDR-TB relatively early,
Providing an attractive combination of speed and sensitivity.
 Currently, three methods exist; the first two being WHO recommended:
1. Cartridge-based NAAT (CB-NAAT)
2. Line probe assay (LPA)
3. Loop-mediated amplification (LAMP).
Laboratory DiagnosisDirect Detection
Cartridge-based nucleic acid amplification test (CBNAAT)
 The CB-NAAT is a semi-quantitative nested real-time PCR which detects
both MTB and RIF resistance directly from clinical specimens.
 It is the WHO-recommended method in 2010 for the diagnosis of both
pulmonary and extrapulmonary TB and for diagnosing paediatric TB.
 Under the current RNTCP guidelines, it is recommended for diagnosis of
 drug resistant-TB (DR-TB) in presumptive DR-TB and
 Upfront diagnosis of TB in key population
Paediatric tuberculosis
Extra-pulmonary cases
People living with HIV.
Laboratory DiagnosisDirect Detection
Cartridge-based nucleic acid amplification test (CBNAAT)
 The analytical limit is 131 CFU/ml and the TAT is 2–3 h.
 Results can be ideally available while patient waits in the clinic.
 Because the cartridges are self-contained, the problem of
cross-contamination between samples is eliminated.
 Sputum is liquefied and inactivated with a sample reagent which kills over
99.9% of TB bacilli in the specimen, and 2 ml of the material is transferred
into a cartridge and this is inserted in the MTB-RIF test platform.
 It uses three specific primers and five unique molecular probes to ensure
high degree of specificity.
 The primers amplify a portion of the rpoB gene 81 bp RIF resistance
determining region.
Laboratory DiagnosisDirect Detection
Cartridge-based nucleic acid amplification test (CBNAAT)
 The probes are capable to differentiate between wild-type (WT) and conserved sequence
and mutations in the core region.
The sensitivity was
99.8% for smear- and culture-positive cases and
90.2% for smear-negative, culture-positive cases.
The MTB/RIF test correctly detected RIF resistance with a sensitivity of 99.1% and 100%
specificity.
 Thus, the test detects TB in essentially all smear-positive samples and the majority of
smear-negative samples.
 The presence of non-tuberculous Mycobacteria does not confound testing.
 The cartridges are stable at room temperature
Limitations of CB-NAAT
 Presence of mono-resistance to INH which is not detected in this test.
Laboratory DiagnosisDirect Detection
Cartridge-based nucleic acid amplification test (CBNAAT)
 INH mono-resistance is documented to be 7%–11% in the first-line treatment failures and
newly diagnosed and previously untreated patients, respectively.
 Both live and dead bacilli are picked up by the CB-NAAT thus making this test in the
current format useless to assess post-therapy efficacy.
 Concerns exist regarding false-positive RIF resistance results;
Samples found to be resistant must be confirmed by
Second Xpert MTB/RIF test or
LPA
Phenotypic culture testing.
 In case an indeterminate result is obtained on the first specimen, a repeat testing of a new
specimen by CBNAAT is required,
 If the result of this is also indeterminate, testing by culture and DST or Line Probe assay
is mandated.
Laboratory DiagnosisDirect Detection
Line Probe Assay (LPA)
 This strip test detects TB DNA and genetic mutations associated with drug resistance
from smear-positive sputum specimens or culture isolates after DNA extraction and PCR
amplification.
 Hybridisation assay that allows differentiation between Mycobacterium species.
Each strip consists of 27 reaction zones (bands), including
6 controls (conjugate, amplification, M. tuberculosis complex, rpoB, katG and inhA
controls),
8 rpoB WT
4 mutants (MUT) probes,
1 katG WT and
2 MUT probes
2 inhA WT
4 MUT probes.
Laboratory DiagnosisDirect Detection
Line Probe Assay (LPA)
 Theoretically the TAT is 5–6 h but the entire procedure usually takes upto 72 hours.
 It has a good sensitivity and specificity when performed on smear-positive and on culture
isolates.
 Sensitivity, specificity and positive and negative predictive values were 98.9%, 99.4%,
97.9% and 99.7% for the detection of RIF resistance; while
 It was 94.2%, 99.7%, 99.1% and 97.9%, respectively, for the detection of INH resistance
and
 WHO has endorsed LPA for MDR-TB in 2009.
Two commercially available products are
(1) InnoLiPA assay-Innogenetics, Belgium, and
(2) Hain Lifescience GenoType® MTBDRplus.
Laboratory DiagnosisDirect Detection
Detection of resistance to the second-line drugs
 At present, the ‘gold standard’ DST method measures phenotypic resistance by the
culture-based indirect proportion method, which has been standardised for solid
and liquid media for the detection of ofloxacin (OFX) and AMK resistance.
 Using these platforms, a DST may take anywhere between 10 days and 6 weeks.
 Excluding second-line drug resistance is a critical prerequisite for identifying
patients who can be placed on the shorter MDR-TB regimen.
 Hain’s MTBDRsl version was developed with this in mind to shorten the TAT of
second-line DST testing to 1–2 days.
These assays detect mutations in the
gyrA gene (fluoroquinolone resistance),
rrs gene (KM, AMK and CM resistance) and
embB gene (EMB resistance).
Laboratory DiagnosisDirect Detection
Detection of resistance to the second-line drugs
 Any smear-positive or MDR culture-positive patient (adult or
children) who has a positive Hain MDRplus assay may undergo the
MTBDRsl version.
 This enables a rapid diagnosis of pre-XDR or XDR-TB in a
smear-positive patient or if an MDR isolate is used.
 The sensitivity for detecting OFX, AMK and extensive drug resistance
directly from clinical samples was 90.7%, 100% and 92.3%,
respectively
 The specificity for detection was 98.1%, 99.4% and 99.6%,
respectively
Laboratory DiagnosisDirect Detection
Loop Mediated Amplification (LAMP)
 Molecular amplification methods are proven technologies for the detection of TB but
have not been widely used in remote settings because of the cost and complexity.
 LAMP is a simple, rapid, specific and cost-effective nucleic acid amplification method
solely developed by Eiken Chemical Co., Ltd, Japan.
 It is characterised by the use of four different primers specifically designed to recognise
six distinct regions on the target gene and
 The reaction process proceeds at a constant temperature using auto-cycling strand
displacement reaction targeting the six regions of the gyrB and 16S rRNA genes.
 LAMP is a simple isothermal DNA amplification method that does not require a
thermocycler or detection system and allows visual detection of amplification, possibly
allowing it to be used at lower levels of the health system.
 It detects M. tuberculosis complex but does not detect resistance.
 The assay had a detection limit of 5–50 copies of purified DNA with a 60-min incubation
time.
TB-LAMP
Laboratory DiagnosisIndirect Detection
Tuberculin skin testing
 Popularly known as Mantoux test (Charles Mantoux, 1912)involves injecting the purified
protein derivative (PPD) of MTB intradermally in the forearm and the resulting reaction
is read after 48–72 h.
 It detects only exposure to MTB or latent TB.
 At present, only two tuberculins have been accepted as standard tuberculins by WHO
PPD-S PPD, prepared according to the method described by Siebert, from MTB and
PPD RT 23.
 PPD-RT 23 with Tween 80 of strength 1 TU and 2 TU is standardised tuberculin available
in India supplied by BCG Vaccine Laboratory, Guindy, Chennai.
 The optimal strength of PPD is 2 TU.
 A positive test is considered when 10 mm or more induration is present.
 However, vaccination with the BCG vaccine can also lead to a reaction at the TST site (as
can repeat TST testing), which limits the test’s usefulness in vaccinated children.
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Laboratory DiagnosisIndirect Detection
Interferon-gamma release assay
 This is an in vitro assay wherein T-cells sensitised with MTB on
encountering mycobacterial antigen
Early secretory antigenic target 6 [ESAT-6] and
Culture filtrate protein 10 [CFP-10] release interferon-gamma (a
TH1 cytokine).
 Advantages of this test are that the antigen used is recognised by T-cells of
TB patients and not by BCG-vaccinated or healthy unvaccinated
individuals.
 It has a very high specificity and much less likely than the TST to be
confounded by exposure to environmental mycobacteria or by prior BCG
vaccination.
 It does not boost responses that will be measured by subsequent tests as
happens with TST.
Laboratory DiagnosisIndirect Detection
Interferon-gamma release assay
 IGRAs do not require a second visit to the clinic to evaluate the test
result, thus potentially reducing costs to the patient.
 Results can be available within 24 h.
Commercially available tests are
QuantiFERON-TB Gold (QFT-G) and
QuantiFERON-TB Gold in Tube (QFT-GIT) (Cellestis, Australia)
T-SPOT TB (Immunotec, UK).
THANK YOU

Mycobacterium tuberculosis

  • 1.
  • 2.
    History of Tuberculosis Tuberculosis is one of the oldest of humankind’s plagues.  Mycobacterium tuberculosis probably emerged as a pathogen of our early ancestors 20,000 to 15,000 years ago in east Africa.  As humans peopled the globe, they took their diseases with them, including tuberculosis.  The writings of classical Greek and Roman physicians make it clear that they recognized tuberculosis.  During the 17th and 18th centuries, tuberculosis exploded with soaring prevalence.  In 1680 John Bunyan described it as “the Captain among these men of death”.  During the next 200 years this sobriquet would hold, as tuberculosis became a leading cause of death in Europe and North America.  A unified concept of tuberculosis first emerged with the work of Lae¨nnec in the early 19th century.
  • 7.
    Mycobacteria- Basic Bacteriology Mycobacteria belong to the family Mycobacteriaceae and the order Actinomycetales.  The organisms that belong to the genus Mycobacterium are Aerobic (although some may grow in reduced oxygen concentrations), Non–spore forming (except for Mycobacterium marinum), Nonmotile, Very thin, slightly curved or straight rods (0.2-0.6 3 1-10 𝛍m).  Some species may display a branching morphology.  Mycobacterium is the only genus in the Mycobacteriaceae family.
  • 8.
    Mycobacteria- Basic Bacteriology Mycobacterium spp. have an unusual cell wall structure.  The cell wall contains N-glycolylmuramic acid instead of N-acetylmuramic acid, and it has a very high lipid content, which creates a hydrophobic permeability barrier.  Because of this cell wall structure, mycobacteria are difficult to stain with commonly used basic aniline dyes, such as those used in Gram staining.  Although these organisms cannot be readily Gram stained, they generally are considered gram positive.  However, they resist decolorization with acidified alcohol (3% hydrochloric acid) after prolonged application of a basic fuchsin dye or with heating of this dye after its application.  This important property of mycobacteria, which derives from their cell wall structure, is referred to as acid fastness; this characteristic distinguishes mycobacteria from other genera.
  • 9.
    Mycobacteria- Basic Bacteriology Another important feature of many species is that they grow more slowly than most other human pathogenic bacteria because of their hydrophobic cell surface.  Because of this hydrophobicity, organisms tend to clump, so that nutrients are not easily allowed into the cell.  A single cell’s generation time (the time required for a cell to divide into two independent cells) may range from approximately 20 hours to 36 hours for Mycobacterium ulcerans.  Slow-growing mycobacteria, by definition, require more than 7 days to produce colonies on solid media.  The variation in generation times among the mycobacteria results in the formation of visible colonies in 2 to 60 days at optimum temperature.  Rapid-growing mycobacteria (RGMs), in which growth is apparent sooner than 7 days after subculture to Lowenstein-Jensen medium, may partially or completely lose this characteristic as a result of their growth characteristics.
  • 10.
    Mycobacterium Tuberculosis Complexand NTMs  Mycobacteria can be divided into two major groups, based on fundamental differences in epidemiology and association with disease: those belonging to the M. tuberculosis complex and the NTM group.  Currently, the genus Mycobacterium includes more than 150 recognized or proposed species that are predominantly classified as nontuberculous environmental mycobacteria (NTM).  There are several species that are prominent pathogens, most notably the Mycobacterium tuberculosis complex, Mycobacterium leprae, and Mycobacterium ulcerans.  In the clinical microbiology laboratory, the term complex is commonly used to describe two or more species for which distinction is complicated and has little or no medical importance.
  • 12.
    Mycobacterium Tuberculosis Complexand NTMs The mycobacterial species that belong to the M. tuberculosis complex M. tuberculosis, Mycobacterium bovis Mycobacterium bovis BCG, Mycobacterium africanum, Mycobacterium caprae, Mycobacterium microti, Mycobacterium canettii, Mycobacterium mungi, Mycobacterium orygis, Mycobacterium pinnipedii.
  • 13.
    Mycobacterium Tuberculosis Complexand NTMs All of these species are capable of causing tuberculosis. It should be noted that species identification might be required for epidemiologic and public health reasons. The organisms that belong to the M. tuberculosis complex are considered slow growers, and colonies are nonpigmented.
  • 15.
    Cell wall of M.tuberculosis
  • 16.
    Epidemiology  More than5 million new cases of tuberculosis (all forms, both pulmonary and extrapulmonary) were reported to the World Health Organization (WHO) in 2005;  >90% of cases were reported from developing countries.  The WHO estimated that 8.8 million new cases of tuberculosis occurred worldwide in 2005,  95% of them in developing countries of Asia (4.9 million), Africa (2.6 million), the Middle East (0.6 million), and Latin America (0.4 million).  It is further estimated that 1.6 million deaths from tuberculosis occurred in 2005, 95% of them in developing countries.  An estimated 1.7 billion people, or one third of the world’s population, are infected with M. tuberculosis.
  • 17.
    Epidemiology  This reservoirof infected individuals results in 8 million new cases of tuberculosis and 2.9 million deaths annually.  Tuberculosis continues to be a public health problem in the United States.  An additional complicating factor in the management of tuberculosis is the increasing incidence of coinfection with the human immunodeficiency virus (HIV).  HIV-associated tuberculosis remains a significant challenge to world health, with an estimated 1.1 million individuals living with HIV-associated tuberculosis.  In the United States, tuberculosis typically is found among the poor, the homeless, intravenous (IV) drug users, alcoholics, the elderly, or medically underserved populations.
  • 18.
    World map ofcountries by tuberculosis (TB) incidence
  • 24.
    FROM EXPOSURE TOINFECTION  M. tuberculosis is most commonly transmitted from a person with infectious pulmonary tuberculosis to others by droplet nuclei, which are aerosolized by coughing, sneezing, or speaking.  The tiny droplets dry rapidly; the smallest (<5–10 μm in diameter) may remain suspended in the air for several hours and may reach the terminal air passages when inhaled.  There may be as many as 3000 infectious nuclei per cough.  Other routes of transmission of tubercle bacilli (e.g., through the skin or the placenta) are uncommon and of no epidemiologic significance. Determinants of the likelihood of transmission The probability of contact with a person who has an infectious form of tuberculosis, The intimacy and duration of that contact, The degree of infectiousness of the case, and The shared environment in which the contact takes place are all important
  • 25.
    FROM EXPOSURE TOINFECTION  Tuberculosis patients whose sputum contains AFB visible by microscopy are the most likely to transmit the infection.  The most infectious patients have cavitary pulmonary disease or, much less commonly, laryngeal tuberculosis and produce sputum containing as many as 105–107 AFB/mL.  Patients with sputum smear–negative/culture-positive tuberculosis are less infectious, and those with culture-negative pulmonary disease and extrapulmonary tuberculosis are essentially non-infectious.  Because persons with both HIV infection and tuberculosis are less likely to have cavitations, they may be less infectious than persons without HIV co-infection.  Crowding in poorly ventilated rooms is one of the most important factors in the transmission of tubercle bacilli, since it increases the intensity of contact with a case.  It is estimated that, in high-prevalence settings, up to 20 contacts may be infected by each AFB-positive case before the index case is found to have tuberculosis.
  • 27.
    FROM INFECTION TODISEASE  The risk of developing disease after being infected depends largely on endogenous factors, such as Individual’s innate immunologic defenses Nonimmunologic defenses Level of function of cell-mediated immunity (CMI).  Clinical illness directly after infection is classified as primary tuberculosis and is common among children up to 4 years of age and among immunocompromised persons.  Although primary tuberculosis may be severe and disseminated, it is not generally associated with high-level transmissibility.  When infection is acquired later in life, the chance is greater that the mature immune system will contain it at least temporarily.
  • 28.
    FROM INFECTION TODISEASE  The majority of infected individuals who ultimately develop tuberculosis do so within the first year or two after infection.  Dormant bacilli, however, may persist for years before reactivating to produce secondary (or post-primary) tuberculosis, which, because of frequent cavitation, is more often infectious than is primary disease.  Overall, it is estimated that up to 10% of infected persons will eventually develop active tuberculosis in their lifetime.  The risk is much higher among HIV-infected persons.  Reinfection of a previously infected individual, which is common in areas with high rates of tuberculosis transmission, may also favor the development of disease.
  • 31.
    PATHOGENESIS- INFECTION AND MACROPHAGEINVASION  The interaction of M. tuberculosis with the human host begins when droplet nuclei containing microorganisms from infectious patients are inhaled.  Although the majority of inhaled bacilli are trapped in the upper airways and expelled by ciliated mucosal cells, a fraction (usually <10%) reach the alveoli.  There, alveolar macrophages that have not yet been activated phagocytize the bacilli.  Invasion of macrophages by mycobacteria results largely from binding of the bacterial cell wall with a variety of macrophage cell-surface molecules, including Complement receptors, Mannose receptor, Immunoglobulin GFcγ receptor, and Type A scavenger receptors
  • 32.
    PATHOGENESIS- INFECTION AND MACROPHAGEINVASION  Phagocytosis is enhanced by complement activation leading to opsonization of bacilli with C3 activation products such as C3b.  After a phagosome forms, the survival of M. tuberculosis within it seems to depend on reduced acidification due to lack of accumulation of vesicular proton-adenosine triphosphatase.  A complex series of events is probably generated by the bacterial cell-wall glycolipid lipoarabinomannan (LAM).  LAM inhibits the intracellular increase of Ca2+.Thus the Ca2+/calmodulin pathway (leading to phagosome-lysosome fusion) is impaired, and the bacilli may survive within the phagosomes.  If the bacilli are successful in arresting phagosome maturation, then replication begins and the macrophage eventually ruptures and releases its bacillary contents.
  • 33.
  • 34.
    INNATE RESISTANCE TOINFECTION  The existence of this resistance, which is polygenic in nature, is suggested by the differing degrees of susceptibility to tuberculosis in different population.  The human gene NRAMP1 (natural resistance–associated macrophage protein 1), which maps to chromosome 2q, may play a role in determining susceptibility to tuberculosis.  Polymorphisms in multiple genes, such as those encoding for Histocompatibility leukocyte antigen (HLA), Interferon γ (IFN-γ), T-cell growth factor β (TGF-β), Interleukin (IL) 10, Mannose-binding protein, IFN-γ receptor, Toll-like receptor (TLR) 2, Vitamin D receptor, and IL-1, have been associated with susceptibility to tuberculosis.
  • 36.
    THE HOST RESPONSE In the initial stage of host-bacterium interaction, either fusion between phagosomes and lysosomes occurs, preventing bacillary survival, or the bacilli begin to multiply, ultimately killing the macrophage. A variety of chemo-attractants that are released after cell lysis Complement components Bacterial molecules Cytokines Recruit additional immature monocyte-derived macrophages, including dendritic cells, which migrate to the draining lymph nodes and present mycobacterial antigens to T lymphocytes.  At this point, the development of CMI and humoral immunity begins.  These initial stages of infection are usually asymptomatic.
  • 37.
    THE HOST RESPONSE About 2–4 weeks after infection, two host responses to M. tuberculosis develop: Macrophage-activating CMI response Tissue-damaging response.  The macrophage activating response is a T-cell–mediated phenomenon resulting in the activation of macrophages that are capable of killing and digesting tubercle bacilli.  The tissue-damaging response is the result of a delayed-type hypersensitivity (DTH) reaction to various bacillary antigens.  It destroys inactivated macrophages that contain multiplying bacilli but also causes caseous necrosis of the involved tissues.  Both of these responses can inhibit mycobacterial growth,  It is the balance between the two that determines the form of tuberculosis that will develop subsequently.
  • 38.
    GRANULOMA FORMATION  Withthe development of specific immunity and the accumulation of large numbers of activated macrophages at the site of the primary lesion, granulomatous lesions (tubercles) are formed.  These lesions consist of accumulations of lymphocytes and activated macrophages that evolve toward epithelioid and giant cell morphologies.  Initially, the tissue-damaging response can limit mycobacterial growth within macrophages.  As stated above, this response, mediated by various bacterial products, not only destroys macrophages but also produces early solid necrosis in the center of the tubercle.  Although M. tuberculosis can survive, its growth is inhibited within this necrotic environment by low oxygen tension and low pH.  At this point, some lesions may heal by fibrosis, with subsequent calcification, whereas inflammation and necrosis occur in other lesions.
  • 39.
    THE MACROPHAGE-ACTIVATING RESPONSE CMI is critical at this early stage.  In the majority of infected individuals, local macrophages are activated when bacillary antigens processed by macrophages stimulate T lymphocytes to release a variety of lymphokines.  These activated macrophages aggregate around the lesion’s center and effectively neutralize tubercle bacilli without causing further tissue destruction.  In the central part of the lesion, the necrotic material resembles soft cheese (caseous necrosis)—a phenomenon that may also be observed in other conditions, such as neoplasms.  Even when healing takes place, viable bacilli may remain dormant within macrophages or in the necrotic material for many years.  These “healed” lesions in the lung parenchyma and hilar lymph nodes may later undergo calcification.
  • 40.
    THE DELAYED-TYPE HYPERSENSITIVITY REACTION In a minority of cases, the macrophage-activating response is weak, and mycobacterial growth can be inhibited only by intensified DTH reactions, which lead to lung tissue destruction.  The lesion tends to enlarge further, and the surrounding tissue is progressively damaged.  At the center of the lesion, the caseous material liquefies.  Bronchial walls as well as blood vessels are invaded and destroyed, and cavities are formed.  The liquefied caseous material, containing large numbers of bacilli, is drained through bronchi.  Within the cavity, tubercle bacilli multiply, spill into the airways, and are discharged into the environment through expiratory maneuvers such as coughing and talking.  In the early stages of infection, bacilli are usually transported by macrophages to regional lymph nodes, from which they gain access to the bloodstream and disseminate widely throughout the body.  In young children with poor natural immunity, hematogenous dissemination may result in fatal miliary tuberculosis or tuberculous meningitis.
  • 44.
    Stages of granuloma formationduring tuberculosis.  Initial phase of Mycobacterium tuberculosis infection leads to induction of innate responses and apoptosis.  The consequential chemotactic signals help recruiting more of uninfected macrophages to the site of infection.  Some of the infected macrophages also egress and seed new granulomas.  The advent of adaptive immunity results in attainment of equilibrium between the pathogen and host immune system.  The overall bacterial load keeps on increasing during granuloma maturation till equilibrium is attained.  When a person is immunocompromised, caseation occurs and rapid bacillary dissemination takes place.
  • 49.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis Tuberculosis is classified as pulmonary, extrapulmonary, or both.  Before the advent of HIV infection, ∼80% of all new cases of tuberculosis were limited to the lungs.  However, up to two-thirds of HIV-infected patients with tuberculosis may have both pulmonary and extrapulmonary disease or extrapulmonary disease alone.  Pulmonary tuberculosis can be categorized as primary or postprimary (secondary). Primary Disease  Primary pulmonary tuberculosis occurs soon after the initial infection with tubercle bacilli, often seen in children.  Because most inspired air is distributed to the middle and lower lung zones, these areas of the lungs are most commonly involved in primary tuberculosis.  The lesion forming after infection is usually peripheral and accompanied in more than half of cases by hilar or paratracheal lymphadenopathy, which may not be detectable on chest radiography.
  • 50.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis In the majority of cases, the lesion heals spontaneously and may later be evident as a small calcified nodule (Ghon lesion).  In children and in persons with impaired immunity (e.g., those with malnutrition or HIV infection), primary pulmonary tuberculosis may progress rapidly to clinical illness.  The initial lesion increases in size and can evolve in different ways.  Pleural effusion (two-thirds of cases) results from the penetration of bacilli into the pleural space from an adjacent subpleural focus.  In severe cases, the primary site rapidly enlarges, its central portion undergoes necrosis, and cavitation develops (Progressive primary tuberculosis).  Tuberculosis in young children is almost invariably accompanied by hilar or mediastinal lymphadenopathy due to the spread of bacilli from the lung parenchyma through lymphatic vessels.  Enlarged lymph nodes may compress bronchi, causing obstruction and subsequent segmental or lobar collapse.
  • 51.
  • 52.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis Partial obstruction may cause obstructive emphysema, and bronchiectasis may also develop.  Hematogenous dissemination, which is common and often asymptomatic, may result in the most severe manifestations of primary M. tuberculosis infection.  Bacilli reach the bloodstream from the pulmonary lesion or the lymph nodes and disseminate into various organs, where they may produce granulomatous lesions.  Although healing frequently takes place, immunocompromised persons (e.g., patients with HIV infection) may develop miliary tuberculosis and/or tuberculous meningitis.
  • 53.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis PostprimaryDisease  Also called adult-type, reactivation, or secondary tuberculosis, postprimary disease results from endogenous reactivation of latent infection.  Usually localized to the apical and posterior segments of the upper lobes, where the substantially higher mean oxygen tension (compared with that in the lower zones) favors mycobacterial growth. The superior segments of the lower lobes are frequently involved.  The extent of lung parenchymal involvement varies greatly, from small infiltrates to extensive cavitary disease.  With cavity formation, liquefied necrotic contents are ultimately discharged into the airways, resulting in satellite lesions within the lungs that may in turn undergo cavitation.  Massive involvement of pulmonary segments or lobes, with coalescence of lesions, produces Tuberculous pneumonia.
  • 54.
  • 55.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis Although up to one third of untreated patients reportedly succumb to severe pulmonary tuberculosis within a few weeks or months after onset (the classical “galloping consumption” of the past),  Others undergo a process of spontaneous remission or proceed along a chronic, progressively debilitating course (“consumption”).  Under these circumstances, some pulmonary lesions become fibrotic and may later calcify, but cavities persist in other parts of the lungs.  Individuals with such chronic disease continue to discharge tubercle bacilli into the environment.  Most patients respond to treatment, with defervescence, decreasing cough, weight gain, and a general improvement in well-being within several weeks.
  • 56.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis Early in the course of disease, symptoms and signs are often nonspecific and insidious, consisting mainly of fever and night sweats, weight loss, anorexia, general malaise, and weakness.  However, in the majority of cases, cough eventually develops—often initially nonproductive and subsequently accompanied by the production of purulent sputum, sometimes with blood streaking.  Massive hemoptysis may ensue as a consequence of the erosion of a blood vessel in the wall of a cavity.  Hemoptysis, however, may also result from rupture of a dilated vessel in a cavity (Rasmussen’s aneurysm) or from aspergilloma formation in an old cavity.  Pleuritic chest pain sometimes develops in patients with subpleural parenchymal lesions.  Extensive disease may produce dyspnea and, in rare instances, adult respiratory distress syndrome (ARDS).
  • 57.
    CLINICAL MANIFESTATIONS- Pulmonary Tuberculosis Physical findings are of limited use in pulmonary tuberculosis. Many patients have no abnormalities detectable by chest examination, whereas  Others have detectable rales in the involved areas during inspiration, especially after coughing.  Occasionally, rhonchi due to partial bronchial obstruction and classic amphoric breath sounds in areas with large cavities may be heard.  Systemic features include fever (often low-grade and intermittent) in up to 80% of cases and wasting.  Absence of fever, however, does not exclude tuberculosis.  In some cases, pallor and finger clubbing develop.  The most common hematologic findings are mild anemia and leukocytosis.  Hyponatremia due to the syndrome of inappropriate secretion of antidiuretic hormone (SIADH) has also been reported.
  • 58.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Lymph-Node Tuberculosis (Tuberculous Lymphadenitis)  The most common presentation of extrapulmonary tuberculosis, lymph-node disease is particularly frequent among HIV-infected patients.  In the United States, children and women (particularly non-Caucasians) also seem to be especially susceptible.  Once caused mainly by M. bovis, tuberculous lymphadenitis is today due largely to M. tuberculosis.  Lymph-node tuberculosis presents as painless swelling of the lymph nodes, most commonly at posterior cervical and supraclavicular sites (a condition historically referred to as Scrofula).  Lymph nodes are usually discrete and nontender in early disease but may be inflamed and have a fistulous tract draining caseous material.
  • 59.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Associated pulmonary disease is seen in >40% of cases.  The diagnosis is established only by fine needle aspiration or surgical biopsy.  AFB are seen in up to 50% of cases, cultures are positive in 70–80%, and histologic examination shows granulomatous lesions.  Among HIV-infected patients, granulomas usually are not seen. Differential diagnosis Lymphomas or metastatic carcinomas, and rare disorders like Kikuchi’s disease (necrotizing histiocytic lymphadenitis), Kimura’s disease, and Castleman’s disease.
  • 62.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Pleural Tuberculosis  Involvement of the pleura, may result from Contiguous spread of parenchymal inflammation, Actual penetration by tubercle bacilli into the pleural space.  Depending on the extent of reactivity, the effusion may be small, remain unnoticed, and resolve spontaneously or may be sufficiently large to cause symptoms such as fever, pleuritic chest pain, and dyspnea.  Physical findings are those of pleural effusion: dullness to percussion and absence of breath sounds.  A chest radiograph reveals the effusion and, in up to one-third of cases, also shows a parenchymal lesion.  Thoracentesis is required to ascertain the nature of the effusion and to differentiate it from manifestations of other etiologies.
  • 63.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis The fluid is  Straw colored and at times hemorrhagic;  It is an exudate with a protein concentration >50% of that in serum (usually ∼4–6 g/dL),  A normal to low glucose concentration,  A pH of ∼7.3 (occasionally <7.2), and  Detectable white blood cells (usually 500–6000/μL).  Neutrophils may predominate in the early stage, whereas mononuclear cells are the typical finding later.
  • 64.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Mesothelial cells are generally rare or absent.  AFB are seen on direct smear in only 10–25% of cases, but cultures may be positive for M. tuberculosis in 25–75% of cases;  Positive cultures are more common among postprimary cases.  Determination of the pleural concentration of adenosine deaminase (ADA) is a useful screening test.  Tuberculosis is virtually excluded if the value is very low.  Needle biopsy of the pleura is often required for diagnosis and reveals granulomas and/or yields a positive culture in up to 80% of cases.
  • 65.
  • 66.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Tuberculous empyema is a less common complication of pulmonary tuberculosis.  It is usually the result of the rupture of a cavity, with spillage of a large number of organisms into the pleural space.  This process may create a bronchopleural fistula with evident air in the pleural space.  A chest radiograph shows hydropneumothorax with an air-fluid level.  The pleural fluid is purulent and thick and contains large numbers of lymphocytes.  Acid-fast smears and mycobacterial cultures are often positive.  Surgical drainage is usually required as an adjunct to chemotherapy.  Tuberculous empyema may result in severe pleural fibrosis and restrictive lung disease.  Removal of the thickened visceral pleura (decortication) is occasionally necessary to improve lung function.
  • 67.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Tuberculosis of the Upper Airways Nearly always a complication of advanced cavitary pulmonary tuberculosis, tuberculosis of the upper airways may involve the larynx, pharynx, and epiglottis. Symptoms include Hoarseness, Dysphonia, and Dysphagia Chronic productive cough.  Findings depend on the site of involvement, and ulcerations may be seen on laryngoscopy.  Acid-fast smear of the sputum is often positive, but biopsy may be necessary in some cases to establish the diagnosis.  Carcinoma of the larynx may have similar features but is usually painless.
  • 68.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Genitourinary tuberculosis, which accounts for ∼15% of all extrapulmonary cases in the United States, may involve any portion of the genitourinary tract. Urinary frequency, Dysuria, Nocturia, Hematuria, and Flank or abdominal pain are common presentations.  Urinalysis gives abnormal results in 90% of cases, revealing pyuria and hematuria.  The documentation of culture negative pyuria in acidic urine raises the suspicion of tuberculosis.  Intravenous pyelography, abdominal CT, or MRI may show deformities and obstructions, and calcifications and ureteral strictures are suggestive findings.
  • 69.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Culture of three morning urine specimens yields a definitive diagnosis in nearly 90% of cases.  Severe ureteral strictures may lead to hydronephrosis and renal damage.  Genital tuberculosis is diagnosed more commonly in female than in male patients.  In female patients, it affects the fallopian tubes and the endometrium and may cause infertility, pelvic pain, and menstrual abnormalities.  Diagnosis requires biopsy or culture of specimens obtained by dilatation and curettage.  In male patients, tuberculosis preferentially affects the epididymis, producing a slightly tender mass that may drain externally through a fistulous tract;  orchitis and prostatitis may also develop.  In almost half of cases of genitourinary tuberculosis, urinary tract disease is also present.
  • 70.
  • 71.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Skeletal Tuberculosis  In bone and joint disease, pathogenesis is related to reactivation of hematogenous foci or to spread from adjacent paravertebral lymph nodes.  Weight-bearing joints (the spine in 40% of cases, the hips in 13%, and the knees in 10%) are most commonly affected.  Spinal tuberculosis (Pott’s disease or tuberculous spondylitis; often involves two or more adjacent vertebral bodies.  Although the upper thoracic spine is the most common site of spinal tuberculosis in children, the lower thoracic and upper lumbar vertebrae are usually affected in adults.  From the anterior superior or inferior angle of the vertebral body, the lesion slowly reaches the adjacent body, later affecting the intervertebral disk.  With advanced disease, collapse of vertebral bodies results in kyphosis (gibbus).
  • 72.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  A paravertebral “cold” abscess may also form.  In the upper spine, this abscess may track to and penetrate the chest wall, presenting as a soft tissue mass.  In the lower spine, it may reach the inguinal ligaments or present as a psoas abscess.  CT or MRI reveals the characteristic lesion and suggests its etiology.  The differential diagnosis includes tumors and Pyogenic bacterial osteomyelitis.  Aspiration of the abscess or bone biopsy confirms the tuberculous etiology, as cultures are usually positive and histologic findings highly typical.  A catastrophic complication of Pott’s disease is paraplegia, which is usually due to an abscess or a lesion compressing the spinal cord.
  • 73.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Paraparesis due to a large abscess is a medical emergency and requires rapid drainage.  Tuberculosis of the hip joints, usually involving the head of the femur, causes pain  Tuberculosis of the knee produces pain and swelling.  If the disease goes unrecognized, the joints may be destroyed.  Diagnosis requires examination of the synovial fluid, which is Thick in appearance, High protein concentration and Variable cell count.  Synovial fluid culture is positive in a high percentage of cases,  Synovial biopsy and tissue culture may be necessary to establish the diagnosis.
  • 76.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Tuberculous Meningitis and Tuberculoma  It is seen most often in young children but also develops in adults, especially those infected with HIV.  Tuberculous meningitis results from the hematogenous spread of primary or postprimary pulmonary disease or from the rupture of a subependymal tubercle into the subarachnoid space.  In more than half of cases, evidence of old pulmonary lesions or a miliary pattern is found on chest radiography. The disease often presents subtly as  Headache and slight mental changes after a  Prodrome of weeks of low-grade fever, malaise, anorexia, and irritability.  If not recognized, tuberculous meningitis may evolve acutely with severe headache, confusion, lethargy, altered sensorium, and neck rigidity.
  • 77.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Paresis of cranial nerves (ocular nerves in particular) is a frequent finding, and the involvement of cerebral arteries may produce focal ischemia.  The ultimate evolution is toward coma, with hydrocephalus and intracranial hypertension. Lumbar puncture is the cornerstone of diagnosis. Cerebrospinal fluid (CSF) examination reveals High leukocyte count (up to 1000/μL), predominance of lymphocytes Sometimes with a predominance of neutrophils in the early stage Protein content of 1–8 g/L (100–800 mg/dL) Low glucose concentration.  However, any of these three parameters can be within the normal range.
  • 78.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  AFB are seen on direct smear of CSF sediment in up to one-third of cases, but repeated lumbar punctures increase the yield.  Culture of CSF is diagnostic in up to 80% of cases and remains the gold standard.  Polymerase chain reaction (PCR) has a sensitivity of up to 80%, but rates of false- positivity reach 10%.  The ADA concentration may be a sensitive test but has low specificity.  Imaging studies (CT and MRI) may show hydrocephalus and abnormal enhancement of basal cisterns or ependyma.  Tuberculoma, an uncommon manifestation of CNS tuberculosis, presents as one or more space-occupying lesions and usually causes seizures and focal signs.  CT or MRI reveals contrast-enhanced ring lesions, but biopsy is necessary to establish the diagnosis.
  • 79.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Gastrointestinal Tuberculosis  Various pathogenetic mechanisms are involved Swallowing of sputum with direct seeding, Hematogenous spread, Ingestion of milk from cows affected by bovine tuberculosis.  Terminal ileum and the cecum are the sites most commonly involved.  Abdominal pain (at times similar to that associated with appendicitis) and swelling,  Obstruction,  Hematochezia  Palpable mass in the abdomen are common findings at presentation.
  • 80.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Fever,  Weight loss,  Anorexia, and  Night sweats are also common.  With intestinal-wall involvement, ulcerations and fistulae may simulate Crohn’s disease; the differential diagnosis with this entity is always difficult.  Anal fistulae should prompt an evaluation for rectal tuberculosis.  As surgery is required in most cases, the diagnosis can be established by histologic examination and culture of specimens obtained intraoperatively.
  • 81.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Tuberculous peritonitis follows either  Direct spread of tubercle bacilli from ruptured lymph nodes and intraabdominal organs (e.g., genital tuberculosis in women)  Hematogenous seeding. Nonspecific abdominal pain Fever Ascites Paracentesis reveals  Exudative fluid with a high protein content and  Leukocytosis that is usually lymphocytic (although neutrophils occasionally predominate).  The yield of direct smear and culture is relatively low.  Peritoneal biopsy (with a specimen best obtained by laparoscopy) is often needed to establish the diagnosis.
  • 84.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Pericardial Tuberculosis (Tuberculous Pericarditis) Due to Direct progression of a primary focus within the pericardium, Reactivation of a latent focus, or Rupture of an adjacent subcarinal lymph node,  Pericardial tuberculosis has often been a disease of the elderly in countries with low tuberculosis prevalence but also develops frequently in HIV-infected patients.  Case-fatality rates are as high as 40% in some series.  The onset may be subacute, although an acute presentation, with dyspnea, fever, dull retrosternal pain, and a pericardial friction rub, is possible.  An effusion eventually develops in many cases.  Cardiovascular symptoms and signs of cardiac tamponade may ultimately appear.
  • 85.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  CT, or MRI shows effusion and thickness across the pericardial space.  A definitive diagnosis can be obtained by pericardiocentesis under echocardiographic guidance.  The pericardial fluid must be submitted for biochemical, cytologic, and microbiologic study.  The effusion is exudative in nature, with a high count of leukocytes (predominantly mononuclear cells).  Hemorrhagic effusion is frequent.  Direct smear examination is very rarely positive.  Culture of pericardial fluid reveals M. tuberculosis in up to two thirds of cases, whereas pericardial biopsy has a higher yield.  High levels of ADA and IFN-γ may also suggest a tuberculous etiology.
  • 87.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Miliary or Disseminated Tuberculosis  Miliary tuberculosis is due to hematogenous spread of tubercle bacilli.  Consequence of primary infection/ reactivation of old disseminated foci.  The lesions are usually yellowish granulomas 1–2 mm in diameter that resemble millet seeds (thus the term miliary, coined by nineteenth-century pathologists).  Fever, night sweats, anorexia, weakness, and weight loss are presenting symptoms in the majority of cases.  At times patients have a cough and other respiratory symptoms due to pulmonary involvement, as well as abdominal symptoms.  Physical findings include hepatomegaly, splenomegaly, and lymphadenopathy.  Eye examination may reveal Choroidal tubercles, which are pathognomonic of miliary tuberculosis, in up to 30% of cases.
  • 88.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Meningismus occurs in <10% of cases.  A rare presentation seen in the elderly is cryptic military tuberculosis, which has a chronic course characterized by Mild intermittent fever Anemia Meningeal involvement preceding death.  An acute septicemic form, Nonreactive miliary tuberculosis, occurs very rarely and is due to massive hematogenous dissemination of tubercle bacilli.  Pancytopenia is common in this form of disease, which is rapidly fatal.  At postmortem examination, multiple necrotic but nongranulomatous (“nonreactive”) lesions are detected.
  • 89.
  • 90.
  • 91.
  • 92.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Less Common Extrapulmonary Forms Ophthalmic Manifestations  Chorioretinitis,  Uveitis,  Panophthalmitis, and  Painful hypersensitivity-related phlyctenular conjunctivitis. Tuberculous otitis  Hearing loss,  Otorrhea, and  Tympanic membrane perforation.  In the nasopharynx, tuberculosis may simulate Wegener’s granulomatosis.
  • 93.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis Cutaneous manifestations Primary infection due to direct inoculation, Abscesses and chronic ulcers, Scrofuloderma, Lupus vulgaris (a smoldering disease with nodules, plaques, and fissures), Miliary lesions, and Erythema nodosum.  Adrenal tuberculosis is a manifestation of disseminated disease presenting rarely as adrenal insufficiency.  Finally, congenital tuberculosis results from transplacental spread of tubercle bacilli to the fetus or from ingestion of contaminated amniotic fluid.  This rare disease affects the liver, spleen, lymph nodes, and various other organs.
  • 94.
  • 95.
  • 96.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Tuberculosis can appear at any stage of HIV infection, and its presentation varies with the stage.  When CMI is only partially compromised, pulmonary tuberculosis presents in a typical manner, with upper-lobe infiltrates and cavitation and without significant lymphadenopathy or pleural effusion. In late stages of HIV infection Primary tuberculosis–like pattern, Diffuse interstitial or miliary infiltrates, Little or no cavitation, Intrathoracic lymphadenopathy, is more common.
  • 97.
    CLINICAL MANIFESTATIONS- Extra PulmonaryTuberculosis  Overall, sputum smears may be positive less frequently among tuberculosis patients with HIV infection than among those without.  The diagnosis of tuberculosis may be unusually difficult, especially in view of the variety of HIV-related pulmonary conditions mimicking tubercu  Extrapulmonary tuberculosis—alone or in association with pulmonary disease—has been documented in 40–60% of all cases in HIV–co-infected individuals.  The most common forms are lymphatic, disseminated, pleural, and pericardial.  Mycobacteremia and meningitis are also frequent, particularly in advanced HIV disease.
  • 100.
  • 101.
  • 104.
    Laboratory Diagnosis Direct DetectionMethods Microscopy  Sputum smear microscopy still remains the basis for diagnosis of TB in developing countries.  The most regular practice is acid-fast staining using carbol fuschin (Z-N stain) and fluorochrome dye-auramine/rhodamine.  It is relatively fast, inexpensive and specific for TB in high incidence areas.  Although highly specific, smear microscopy is insensitive – it detects roughly 50% of all the active cases of TB (10,000 bacilli/ml need to be present).  Sensitivity can be as low as 20% in children and HIV-infected people.  As per the current Revised National Tuberculosis Control Programme (RNTCP) guidelines, the patient should visit the clinic at least twice to submit a spot – early morning or spot-spot specimen.  At least two ml specimen should be collected which should be mucopurulent.  Sputum specimens should be examined within two days of collection.
  • 105.
    Laboratory Diagnosis Direct DetectionMethods Microscopy  Routine microscopy cannot differentiate between live and dead bacilli and hence cannot be used as a follow-up diagnostic test.  It can neither be used to predict MDR nor the presence of non-tuberculous mycobacteria.  Despite the multitude of disadvantages, in the absence of better alternatives, it is a useful tool in the basic laboratories common in developing countries.  RNTCP has revised the diagnostic algorithm to allow for nucleic acid amplification detection based on cartridge based technologies (CBNAAT) for cases who are smear positive with presumptive MDR-TB/ or living in high MDR- TB areas (>5% and >20% among new and retreatment cases respectively).  It also allows simultaneous testing of second specimen by the above mentioned cartridge based technology for smear negative cases with radiological abnormalities and even those solely based on high clinical suspicion in spite of negative CXR and smear.
  • 108.
    Laboratory Diagnosis Direct DetectionMethods Microscopy Fluorescent microscopy with light-emitting diodes  Light-emitting diodes (LEDs) are more robust, sustainable and user-friendly, thus allowing advantages of FM at peripheral health-care systems. Advantages Extremely long life expectancy. Furthermore, they do not produce ultraviolet (UV) light Do not require darkened rooms and Significantly decrease the instrument’s power consumption Longer lasting battery life.  FM increases the sensitivity of smear microscopy as it allows a much larger area of the smear to be seen, resulting in more rapid examination of the specimen (up to four times faster).
  • 110.
    Laboratory Diagnosis Direct DetectionMethods Microscopy  RNTCP has adopted LED microscopy to replace ZN method in its designated microscopy centres (DMCs) across India.  Instability of fluorescent stains under field conditions and instability of the stained smears for blinded rechecking have been reported. Vital fluorescent staining  Monitoring the response to TB treatment is essential for early detection of treatment failure or drug resistance.  Recent studies proposed a simple and instant method for TB treatment monitoring, based on a common fluorescent viability marker, fluorescein diacetate (FDA), in combination with smear microscopy.  Unlike most fluorescent stains, FDA stains only living, cultivable bacteria thus guiding antimicrobial therapy before culture reports come in.
  • 112.
    Laboratory Diagnosis Direct DetectionMethods Microscopy Newer microscopic technologies  Automated microscopic technology by TBDx (Signature Mapping Medical Sciences, USA) integrates robotic loading of stained slides and automated high-resolution digital image analysis to provide a result in minutes.  The system has a 200-slide capacity reducing the burden on technicians.  Early studies suggested improved sensitivity over the human eye, but specificity was reduced;  Manual review of positive slides was necessary.  A second innovation to assist a microscopist is CellScope, a portable digital FM that provides enlarged digitalised images for review
  • 113.
  • 114.
    Laboratory Diagnosis Direct DetectionMethods Culture  Culture still remains the gold standard for diagnosis of TB  It permits the diagnosis of drug resistance, including the emerging mutations.  Traditional egg-based (Lowenstein-Jensen) and agar-based (Middlebrook 7H10/11) methods are widely used.  The limit of detection is 100 bacilli/ml, thus increasing the sensitivity compared to smear.  the growth in a conventional egg-based medium takes anywhere from 4 to 8 weeks with an additional 4 weeks for drug sensitivity by the conventional proportion method.  Thus, it takes a median of 70 days to diagnose a case of MDR-TB by conventional culture methods.  Other limitations include requirement of biosafety facilities that are expensive to build and maintain and specially trained laboratory technicians to perform the procedure.  Hence, TB cultures are performed only at national reference laboratories
  • 115.
    Laboratory Diagnosis Direct DetectionMethods Culture  Mostly reserved for treatment failure and drug-resistant cases.  Specimens often need to be sent to distant laboratories leading to delay in processing.  Currently WHO/ RNTCP Recommend liquid culture using Middlebrook 7H9 broth – Mycobacterial growth indicator tube (MGIT), a non-radiometric detection method which measures the consumption of oxygen by fluorescence.  As bacteria grow in the culture, the oxygen is utilised causing it to be fluorescent when placed under UV light.  Methods for testing for drug susceptibility follow the same principle but use two culture samples: One with a drug added One without the drug (a growth control)  It is called the Modified 1% proportion sensitivity testing method (PST).
  • 116.
    Laboratory Diagnosis Direct DetectionMethods Culture  In cases of rifampicin resistance (by CBNAAT Test), DST results of all the drugs should be made available.  If the test drug is active against the TB bacteria, it will inhibit growth and suppress fluorescence.  Automated systems have the capacity for up to 960 cultures at a time.  Liquid culture systems provide results significantly faster Diagnosis can be performed in 9 days for a smear-positive case 16 days for a smear-negative case. Negative result is issued by 42 days. DST takes an average 7–14 days after the initial culture.  Automated systems can benefit laboratories with a high workload and provide standardised reading of samples.
  • 117.
    Laboratory Diagnosis Direct DetectionMethods Culture  Such systems have a sensitivity and specificity of nearly 100%.  Both automated and manual systems perform well in the detection of INH and RIF susceptibility but are not as effective for ethambutol (EMB) and streptomycin.  Liquid media are more prone to contamination than solid media, leading to invalid results unless carefully controlled.  Internal quality control of culture involves testing of each batch for sterility and quality strain H37Rv for growth parameters.  For DST Sensitive strain (H37Rv) and mono-resistant strains are tested batch wise.
  • 121.
  • 122.
    Laboratory Diagnosis Direct DetectionRapid identification of species.  Rapid speciation is necessary for the isolates grown in culture to differentiate between M. tuberculosis (MTB) complex and other species of Mycobacteria.  Conventional biochemical methods of speciation using para-nitrobenzoic acid can take weeks.  Strip speciation test can detect a TB-specific antigen (MPT 64) from positive liquid or solid cultures to confirm the presence of organisms belonging to M. tuberculosis complex.  M. tuberculosis protein 64 (MPT-64) antigen is an M. tuberculosis complex (MTBC)- specific antigen secreted during bacterial growth.  This test provides results within 15 min and is highly sensitive and specific.  Sensitivity and specificity were found to be 98.6% and 97.9%, respectively, for the Capilia TB assay (Taunus, Japan).  The intermediate reference laboratories (IRLs) in India utilize this antigen detection for rapid identification of M. tuberculosis complex.
  • 124.
    Laboratory Diagnosis Direct DetectionAntigen Detection  Lipoarabinomannan (LAM) is a 17.5 kD glycolipid found in the outer cell wall of mycobacterial species.  It is immunogenic and a major virulence factor promoting survival in human host.  The test is available as an ELISA or dipstick method with a turnaround time (TAT) of 4–6 h or 20 min depending on the test kit used.  The WHO recommends that it should not be used for the diagnosis of TB, except for HIV-positive in-patients with signs and symptoms of TB (pulmonary and/or extrapulmonary) Who have a CD4 cell count ≤100 cells/μL or, HIV-positive patients who are seriously ill, regardless of the CD4 count.
  • 125.
    Laboratory Diagnosis Direct DetectionAntigen Detection  For TB diagnosis among symptomatic patients, overall lateral flow-LAM pooled sensitivity was 44% and pooled specificity was 92%.  Higher sensitivity of urine LAM detection in patients with HIV Higher bacillary burden and antigen load, Greater likelihood of TB in the genitourinary tract and Greater glomerular permeability that allows increased antigen levels in urine.
  • 127.
    Laboratory Diagnosis Direct DetectionMolecular detection:NAATs  Most molecular methods that are WHO endorsed detect the nucleic acid (DNA) of both live and dead bacilli.  While molecular methods cannot as yet completely replace culture and phenotypic DST, implementation of these assays Reduces the need for costly laboratory infrastructure and Detect MDR-TB relatively early, Providing an attractive combination of speed and sensitivity.  Currently, three methods exist; the first two being WHO recommended: 1. Cartridge-based NAAT (CB-NAAT) 2. Line probe assay (LPA) 3. Loop-mediated amplification (LAMP).
  • 128.
    Laboratory DiagnosisDirect Detection Cartridge-basednucleic acid amplification test (CBNAAT)  The CB-NAAT is a semi-quantitative nested real-time PCR which detects both MTB and RIF resistance directly from clinical specimens.  It is the WHO-recommended method in 2010 for the diagnosis of both pulmonary and extrapulmonary TB and for diagnosing paediatric TB.  Under the current RNTCP guidelines, it is recommended for diagnosis of  drug resistant-TB (DR-TB) in presumptive DR-TB and  Upfront diagnosis of TB in key population Paediatric tuberculosis Extra-pulmonary cases People living with HIV.
  • 129.
    Laboratory DiagnosisDirect Detection Cartridge-basednucleic acid amplification test (CBNAAT)  The analytical limit is 131 CFU/ml and the TAT is 2–3 h.  Results can be ideally available while patient waits in the clinic.  Because the cartridges are self-contained, the problem of cross-contamination between samples is eliminated.  Sputum is liquefied and inactivated with a sample reagent which kills over 99.9% of TB bacilli in the specimen, and 2 ml of the material is transferred into a cartridge and this is inserted in the MTB-RIF test platform.  It uses three specific primers and five unique molecular probes to ensure high degree of specificity.  The primers amplify a portion of the rpoB gene 81 bp RIF resistance determining region.
  • 130.
    Laboratory DiagnosisDirect Detection Cartridge-basednucleic acid amplification test (CBNAAT)  The probes are capable to differentiate between wild-type (WT) and conserved sequence and mutations in the core region. The sensitivity was 99.8% for smear- and culture-positive cases and 90.2% for smear-negative, culture-positive cases. The MTB/RIF test correctly detected RIF resistance with a sensitivity of 99.1% and 100% specificity.  Thus, the test detects TB in essentially all smear-positive samples and the majority of smear-negative samples.  The presence of non-tuberculous Mycobacteria does not confound testing.  The cartridges are stable at room temperature Limitations of CB-NAAT  Presence of mono-resistance to INH which is not detected in this test.
  • 131.
    Laboratory DiagnosisDirect Detection Cartridge-basednucleic acid amplification test (CBNAAT)  INH mono-resistance is documented to be 7%–11% in the first-line treatment failures and newly diagnosed and previously untreated patients, respectively.  Both live and dead bacilli are picked up by the CB-NAAT thus making this test in the current format useless to assess post-therapy efficacy.  Concerns exist regarding false-positive RIF resistance results; Samples found to be resistant must be confirmed by Second Xpert MTB/RIF test or LPA Phenotypic culture testing.  In case an indeterminate result is obtained on the first specimen, a repeat testing of a new specimen by CBNAAT is required,  If the result of this is also indeterminate, testing by culture and DST or Line Probe assay is mandated.
  • 133.
    Laboratory DiagnosisDirect Detection LineProbe Assay (LPA)  This strip test detects TB DNA and genetic mutations associated with drug resistance from smear-positive sputum specimens or culture isolates after DNA extraction and PCR amplification.  Hybridisation assay that allows differentiation between Mycobacterium species. Each strip consists of 27 reaction zones (bands), including 6 controls (conjugate, amplification, M. tuberculosis complex, rpoB, katG and inhA controls), 8 rpoB WT 4 mutants (MUT) probes, 1 katG WT and 2 MUT probes 2 inhA WT 4 MUT probes.
  • 134.
    Laboratory DiagnosisDirect Detection LineProbe Assay (LPA)  Theoretically the TAT is 5–6 h but the entire procedure usually takes upto 72 hours.  It has a good sensitivity and specificity when performed on smear-positive and on culture isolates.  Sensitivity, specificity and positive and negative predictive values were 98.9%, 99.4%, 97.9% and 99.7% for the detection of RIF resistance; while  It was 94.2%, 99.7%, 99.1% and 97.9%, respectively, for the detection of INH resistance and  WHO has endorsed LPA for MDR-TB in 2009. Two commercially available products are (1) InnoLiPA assay-Innogenetics, Belgium, and (2) Hain Lifescience GenoType® MTBDRplus.
  • 137.
    Laboratory DiagnosisDirect Detection Detectionof resistance to the second-line drugs  At present, the ‘gold standard’ DST method measures phenotypic resistance by the culture-based indirect proportion method, which has been standardised for solid and liquid media for the detection of ofloxacin (OFX) and AMK resistance.  Using these platforms, a DST may take anywhere between 10 days and 6 weeks.  Excluding second-line drug resistance is a critical prerequisite for identifying patients who can be placed on the shorter MDR-TB regimen.  Hain’s MTBDRsl version was developed with this in mind to shorten the TAT of second-line DST testing to 1–2 days. These assays detect mutations in the gyrA gene (fluoroquinolone resistance), rrs gene (KM, AMK and CM resistance) and embB gene (EMB resistance).
  • 138.
    Laboratory DiagnosisDirect Detection Detectionof resistance to the second-line drugs  Any smear-positive or MDR culture-positive patient (adult or children) who has a positive Hain MDRplus assay may undergo the MTBDRsl version.  This enables a rapid diagnosis of pre-XDR or XDR-TB in a smear-positive patient or if an MDR isolate is used.  The sensitivity for detecting OFX, AMK and extensive drug resistance directly from clinical samples was 90.7%, 100% and 92.3%, respectively  The specificity for detection was 98.1%, 99.4% and 99.6%, respectively
  • 140.
    Laboratory DiagnosisDirect Detection LoopMediated Amplification (LAMP)  Molecular amplification methods are proven technologies for the detection of TB but have not been widely used in remote settings because of the cost and complexity.  LAMP is a simple, rapid, specific and cost-effective nucleic acid amplification method solely developed by Eiken Chemical Co., Ltd, Japan.  It is characterised by the use of four different primers specifically designed to recognise six distinct regions on the target gene and  The reaction process proceeds at a constant temperature using auto-cycling strand displacement reaction targeting the six regions of the gyrB and 16S rRNA genes.  LAMP is a simple isothermal DNA amplification method that does not require a thermocycler or detection system and allows visual detection of amplification, possibly allowing it to be used at lower levels of the health system.  It detects M. tuberculosis complex but does not detect resistance.  The assay had a detection limit of 5–50 copies of purified DNA with a 60-min incubation time.
  • 142.
  • 143.
    Laboratory DiagnosisIndirect Detection Tuberculinskin testing  Popularly known as Mantoux test (Charles Mantoux, 1912)involves injecting the purified protein derivative (PPD) of MTB intradermally in the forearm and the resulting reaction is read after 48–72 h.  It detects only exposure to MTB or latent TB.  At present, only two tuberculins have been accepted as standard tuberculins by WHO PPD-S PPD, prepared according to the method described by Siebert, from MTB and PPD RT 23.  PPD-RT 23 with Tween 80 of strength 1 TU and 2 TU is standardised tuberculin available in India supplied by BCG Vaccine Laboratory, Guindy, Chennai.  The optimal strength of PPD is 2 TU.  A positive test is considered when 10 mm or more induration is present.  However, vaccination with the BCG vaccine can also lead to a reaction at the TST site (as can repeat TST testing), which limits the test’s usefulness in vaccinated children.
  • 144.
  • 145.
    Laboratory DiagnosisIndirect Detection Interferon-gammarelease assay  This is an in vitro assay wherein T-cells sensitised with MTB on encountering mycobacterial antigen Early secretory antigenic target 6 [ESAT-6] and Culture filtrate protein 10 [CFP-10] release interferon-gamma (a TH1 cytokine).  Advantages of this test are that the antigen used is recognised by T-cells of TB patients and not by BCG-vaccinated or healthy unvaccinated individuals.  It has a very high specificity and much less likely than the TST to be confounded by exposure to environmental mycobacteria or by prior BCG vaccination.  It does not boost responses that will be measured by subsequent tests as happens with TST.
  • 146.
    Laboratory DiagnosisIndirect Detection Interferon-gammarelease assay  IGRAs do not require a second visit to the clinic to evaluate the test result, thus potentially reducing costs to the patient.  Results can be available within 24 h. Commercially available tests are QuantiFERON-TB Gold (QFT-G) and QuantiFERON-TB Gold in Tube (QFT-GIT) (Cellestis, Australia) T-SPOT TB (Immunotec, UK).
  • 152.