Tuberculosis (TB) is an old disease; Genus Mycobacterium had originated more than 150 million years ago (Hayman 1984; Daniel 2006). Egyptian mummies had skeletal abnormalities characteristic of TB and their ancient art depicted Pott’s deformities (Cave 1939; Morse et al. 1964). Even after so many years, TB is still a major global health problem.

World Health Organization (WHO) declared TB as the leading cause of death from a single infectious agent and one of the top ten causes of death worldwide (Global tuberculosis report 2020. 2020). According to the WHO global TB report 2020, globally an estimated 10 million people developed TB and 1.4 million died (Plan and to End TB, 2018–2022. 2019, United Nations; 2020).

Currently, India is at the first position among the eight counties carrying a high burden of Mycobacterium tuberculosis (MTB) in the world (World Health Organization. 2016). India accounts for 36% of global TB deaths among Human immunodeficiency virus (HIV)-negative people, and for 31% of the combined total number of TB deaths in HIV-negative and HIV-positive people (Global tuberculosis report 2020. 2020).

WHO has classified TB based on anatomical site of disease as Pulmonary Tuberculosis (PTB) and extrapulmonary tuberculosis (EPTB) (World 2013). EPTB is an equally important manifestation of TB which remains undiagnosed due to diagnostic challenges in developing countries. EPTB most frequently manifests as peripheral lymphadenopathy and it can involve any organ of the body including brain, skin, soft tissues, small and large intestine, appendix and genitourinary tract (World 2013).

EPTB represented 16% of the 7.1 million incident cases in 2019 (Global tuberculosis report 2020. 2020). Lymph node TB (LNTB, also called TB lymphadenitis) is the most common form of EPTB in India, accounting for around 35% of EPTB cases. The estimated incidence of TB in India was 2.1 million cases in 2019, out of which 385,254 people have EPTB (Global tuberculosis report 2020. 2020; Central TB division. 2020).

Cytology and conventional smear microscopy for acid fast bacilli (AFB) are used as the initial diagnostic tools for LNTB in resource poor settings. Fine needle aspiration cytology (FNAC) is a simple and rapid diagnostic technique (Corbett et al. 2003) but r cytomorphological features of LNTB can overlap with few other lesions other than TB (Sarfaraz et al. 2018). Conventional smear microscopy for AFB lacks sensitivity due to the pauci-bacillary nature of fine needle aspirates (FNA) (Tadesse et al. 2015; Shetty et al. 2020). Isolation of the organism in EPTB by culture remains a gold standard, but it has major limitation of turnaround time of 2–4 weeks leading to a delay in the commencement of anti-tuberculosis treatment (ATT). Considering these limitations, more rapid and reliable methods were needed.

In December 2010, WHO introduced the use of the GeneXpert MTB-RIF for detecting TB (Dewan et al. 2015). In India, it was adopted by Revised National TB Control Programme (RNTCP) in 2012 and the first pilot project was started in Maharashtra state, India (Pamra et al. 1987). The GeneXpert MTB-RIF is a real-time nucleic acid amplification test (NAAT) that simultaneously detects the DNA of MTB and the rpoB mutation associated with rifampicin resistance. It requires minimal technical expertise and has a turnaround time of less than 2 h (World Health Organization 2011). It can be readily performed on the aspirated samples for detection of MTB and helps in ruling out other cytomorphological mimics. GeneXpert MTB-RIF can detect as low bacterial load as 100–130 bacilli per ml of sample makes it ideal for paucibacillary tuberculosis. GeneXpert MTB-RIF is at par with culture which demands 100 bacilli per ml of sample (Manju and Madhusudhan 2020).

Nowadays, Xpert MTB/RIF assay is the most commonly used rapid diagnostic test worldwide. (Global tuberculosis report 2020. 2020). WHO recommends the use of Xpert MTB/RIF to improve the diagnosis of TB and rifampicin resistance in patients with various forms of EPTB (WHO consolidated guidelines on tuberculosis 2020).

WHO defines a bacteriologically confirmed case of TB as one from whom a biological specimen is positive by smear microscopy, culture or WHO-recommended rapid diagnostic test, such as the GeneXpert MTB-RIF assay (Global tuberculosis report 2020. 2020). The diagnostic accuracy of GeneXpert MTB-RIF for pulmonary TB has been reported high but the diagnostic performance-related data for lymph node specimens from high TB burden regions are limited.

More studies are needed in settings with high EPTB burden. We aimed to correlate the different cytomorphological patterns in a clinically suspected case of LNTB with GX and ZN. We tried to suggest the best possible combination of tests that will maximize the detectability in resource limited settings.

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