Rapid diagnosis of drug-resistant tuberculosis (DR-TB) is very challenging, specifically in extra-pulmonary TB specimens. The current study was performed on non-sputum specimens. All specimens were subjected on Xpert MTB/RIF Ultra followed by Xpert MTB/XDR, Ziehl-Neelsen (ZN) Staining, liquid culture, line probe assay (LPA), and drug susceptibility testing (DST). Out of 1,152 non-sputum specimens, 218 were observed to be positive on Xpert MTB/RIF Ultra and were selected for further investigation. From 218 MTBC positive, Xpert MTB/XDR yielded 174 (79.8%) positive while 25 (11.5%) were negative. On comparison with reference standards, ZN smear, and culture, the sensitivity was 100% and 95.51% with specificity of 17.86% and 18.63%, respectively. DST sensitivity and specificity were 84.62% and 96.61%, 83.33% and 96.88%, 50% and 98.75%, 50% and 98.72%, and 50% and 98.75%, respectively, for isoniazid, fluoroquinolones, amikacin, kanamycin, and capreomycin in culture positive specimens. The sensitivity and specificity of Xpert MTB/XDR assay, compared with LPA (MTBDRplus and MTBDRsl), was between 94.12%-100% and 98.39%-100%, respectively. Sensitivity and specificity of Xpert MTB/XDR matched with culture-DST and LPA results for all the tested drugs. Its placement in diagnostic algorithms with Xpert MTB/RIF Ultra under National TB Programs will enhance patient outcome by providing prompt switch to a DST guided treatment regimen. IMPORTANCE This study provides crucial evidence supporting the use of Xpert MTB/XDR for rapid detection of DR-TB in non-sputum specimens including extra-pulmonary specimens, where diagnosis remains challenging due to paucibacillary in nature. By demonstrating high sensitivity and specificity compared with culture-DST and LPA, the assay shows strong potential to be integrated into the National TB Elimination Program (NTEP) diagnostic algorithm. Early detection of resistance to isoniazid, fluoroquinolones, and second-line injectables enables timely transition to DST-guided treatment, reducing delays and improving patient outcomes. The findings highlight the assay's ability to reduce dependency on conventional laboratory-based DST, shortening turnaround time and strengthening decentralized diagnostic capacity. This study provides programmatic evidence for policy-level adoption, supporting India's efforts toward DR-TB control and elimination.

Background Household contacts (HHCs) of MDR-TB patients are at increased risk of developing TB infection (TBI) as well as TB disease. Early identification of TBI is crucial for prevention of TB disease, however Indian data on MDR-TB contacts is limited. Methods We conducted a prospective cohort study (February 2022 to September 2024) in a tertiary care centre enrolling patients from urban slum neighborhoods of New Delhi. 147 HHCs of 36 MDR-TB cases were enrolled for the study and underwent a tuberculin skin test (TST). TBI was defined as TST ≥ 10 mm. Contacts were followed for 2 years for incidence of TB disease. Information on potential risk factors and other co-morbidities such as body mass index, smoking, alcohol consumption, diabetes, hypertension and household overcrowding were recorded. Results TST positivity was seen in 24.48% (36/147) HHCs. During follow-up of 2 years, 5 of 36 TST-positive HHCs (16.67%) developed TB as compared to 1 of 91 TST-negative (1.1%) HHCs. The relative risk of developing TB was 12.75 times higher for TST-positive versus TST-negative HHCs. TB incidence was significantly higher in overcrowded households and among younger or underweight HHCs. Conclusions Our study reinforces the high risk of transmission of MDR-TB to household contacts. Potential risk factors for TB infection include younger, malnourished HHCs with low BMI and household overcrowding. These findings underscore an urgent need to strengthen contact screening and implement targeted interventions in order to curb transmission of tuberculosis amongst contacts.

Abstract Background Early detection of carbapenem-resistant gram negative bacilli(CR-GNB) is critical in patients with sepsis. Delay in diagnosis leads to higher mortality. We evaluated the performance of the Xpert® Carba-R assay (Cepheid, Sunnyvale, CA, USA) directly on flagged blood culture samples in patients with sepsis.Fig 1:Workflow Methods Patients with suspected sepsis with GNB on flagged blood culture were recruited. Xpert® Carba-R assay was performed directly on the positive sample. Their diagnostic performance was compared with culture and drug susceptibility testing (DST)(VITEK-2) and time to results were noted and compared.Table 1:Organism profile of patients with sepsis (n=57) Results In the study, 57 patients were included; Stenotrophomonas maltophila (n=17; 29.8%) was found to be the predominant isolate, which was excluded from analysis (being intrinsically resistant to carbapenems). This was followed by Klebsiella pneumoniae (n=14 ; 24.5%), Acinetobacter baumannii (n=10 ;17.5%), Escherichia coli (n=6;10.5%), Pseudomonas mendonica (n=3; 5.2%), Pseudomonas aeruginosa (n=2;3.5%) and 1 each of Salmonella typhi, Serratia sp., Enterobacter cloacae, Acinetobacter dendrificans, and Enterobacter sp. Xpert® Carba-R positivity was seen in 23/40 isolates (57.5%), and CR GNB was found in 25/40 isolates (62.5%) on routine DST. Discordant results were seen in 6/40 isolates (15%). Overall sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, and negative likelihood ratio of Xpert® Carba-R compared to routine DST (Disk diffusion method and VITEK-2) were 84%, 86.6% , 91.3%, 76.47 %, 6.30 and 0.18 respectively. On genomic analysis, most common CR gene expression was co-expression of NDM and OXA-48 [10/23 (43.5%)], followed by NDM [9/23 (39.1%)] and OXA-48 [4/23 (17.4%)]. The median time to obtain Carba-R result was 44 hours compared to 97 hours for detection of carbapenem resistance in routine DST, giving a 53-hour lead time.Table 2:Comparison of direct Xpert® Carba-R and DST ( disc diffusion method and Vitek-2) in various organisms Conclusion Xpert® Carba-R was found to have a good diagnostic performance for detection of carbapenem resistance when performed directly on positive blood culture samples with substantial time advantage over conventional methods.Fig 2:Distribution of Carbapenem resistant genes*Two discordant sampleCRO- Carbapenem resistant organismCSO- Carbapenem sensitive organism Disclosures All Authors: No reported disclosures

BACKGROUND:Tuberculosis (TB) is caused due to the infection of Mycobacterium tuberculosis (MTB) and it can infect the various parts of the human body. The disease is highly prevalent and is the second most common cause of death worldwide after COVID-19. Apart from sputum specimen, it is exceedingly difficult to diagnose due to its paucibacillary nature. The current study was intended to evaluate the accuracy of Smart Sure™ MTB and multidrug-resistant-TB (MDR-TB) kits (Genetix Biotech Asia Pvt. Ltd., India) with Xpert ultra and Mycobacterium growth indicator tube (MGIT) culture on nonsputum specimens from TB suspects. METHODS:A total of 205 nonsputum specimens were received between October 2023 and May 2024 at Intermediate Reference Laboratory, Department of Medicine, All India Institute of Medical Sciences, New Delhi, India. Xpert ultra and Smart Sure™ MTB and MDR-TB tests were done directly on samples. However, processed specimens were used for MGIT culture and drug-susceptibility testing (DST). Invalid and MGIT contaminated specimens were excluded from the final calculation. RESULTS:Overall, sensitivity and specificity of Smart Sure™ MTB screening kit was 71.59% and 98.28%, respectively, with Xpert ultra and 68.35% and 90.83%, respectively, with MGIT culture. While comparing with both Xpert ultra and MGIT-DST to detect rifampicin (RIF) resistant, Smart Sure™ MDR-TB kits showed sensitivity of 75.0% and 100% of specificity. However, for isoniazid (INH) resistance, Smart Sure™ MDR-TB kits showed 100% of sensitivity and specificity with MGIT-DST. CONCLUSION:For the detection of MTB and its drug-resistance patterns (RIF and INH) in the specimens other than sputum, Smart Sure™ MTB and MDR-TB kits could play a vital role in TB endemic countries. While comparing the set-ups and skilled staffs, it required almost same as compared with previously approved WHO diagnostics used in resource-limited countries.

Background: Tuberculosis (TB) is still the second causative agent of death worldwide after COVID-19. It is caused by Mycobacterium tuberculosis (MTB) infection. Objective: The aim of the current study was to compare the performance of GeneNAT real-time polymerase chain reaction analyzer and pre-loaded chip-based MTB screening and multidrug-resistant tuberculosis (MDR-TB) detection kit (Smart SureTM TM MTB & MDR-TB, Genetix Biotech Asia Pvt. Ltd., New Delhi, India) against the established WHO-approved GeneXpert Ultra (MTB/rifampicin (RIF)), line probe assay (LPA), and mycobacteria growth indicator tube (MGIT) culture at point of care (POC) level. Methods: A total of 450 pulmonary TB (PTB) suspect patients were enrolled from October 2023 to March 2024 at the Intermediate Reference Laboratory, Department of Medicine, All India Institute of Medical Sciences, New Delhi, India. GeneXpert and GeneNAT tests were done directly from sputum specimens. However, processed sputum specimens were used for both LPA (GenoType MTBDRplus) and liquid culture and drug susceptibility testing (MGIT culture and drug susceptibility testing (DST)). Results: On comparing with GeneXpert, for the detection of MTB and rifampicin (RIF), Smart Sure TM showed a sensitivity of 98.18% and 97.5% with a specificity of 100% and 98.92%, respectively. While comparing mutations in the rpoB gene with LPA, the Smart SureTM TM MDR-TB kit exhibited sensitivity and specificity of 96.77% and 99.12%, respectively. For katG and inhA genes, sensitivity and specificity were 97.6% & 85.71% and 98.66% & 98.01%, respectively, for both genes. Smart SureTM TM MDR-TB showed comparable results with MGIT-DST with sensitivity and specificity of 96.88% & 96.15% and 98.99% & 99.02%, respectively, for both RIF and isoniazid (INH) drugs. Conclusion: The GeneNAT system test may provide the status of RIF and INH resistance in PTB cases in a short time with the use of minimal specimens. It required very little infrastructure with less skilled laboratory staff in comparison with other WHO-approved diagnostics used in resource-limited countries with TB and drug-resistant TB burdens.

BACKGROUND:Resource-limited settings like India need a simple, quick, and temperature-independent point-of-care diagnostic test that can diagnose tuberculous meningitis (TBM) at the earliest.METHODS:A prospective study was carried out at a tertiary care center in North India wherein 50 subjects suspected of TBM were recruited and followed up for six months between January 2019 and December 2020. The aim was to evaluate the performance of loop-mediated isothermal amplification (TB-LAMP) in diagnosing TBM as compared to a composite reference standard (CRS), mycobacteria growth indicator tube 960 (MGIT 960) culture, and GeneXpert®.RESULTS:Out of 50 patients, 32 were TBM cases (64%), and 18 were non-TBM cases (36%). The sensitivity of TB-LAMP and GeneXpert® for TBM diagnosis against CRS was 53% (17/32) for both, and the specificity was 78% (14/18) and 89% (16/18), respectively. On comparing TB-LAMP against GeneXpert® for TBM diagnosis, the two methods had almost perfect agreement (Cohen's kappa=0.83) with statistical significance (p<0.001).CONCLUSION:The performance of TB-LAMP assay is comparable to GeneXpert® in diagnosing TBM, and it may be used as a substitute for CSF GeneXpert® in resource-limited settings.

Abstract Background The aim of this study is to evaluate the occurrence of paradoxical reactions (PRs), cytokine levels and outcome in HIV-negative lymphnode tuberculosis (TB) patients. Methods This is a prospective observational study conducted at the All-India Institute of Medical Sciences in New Delhi, India from July 2019 to June 2021. 144 subjects with confirmed or probable lymph node TB, excluding MDR TB, were recruited. Baseline characteristics, clinical presentation, imaging, laboratory parameters, and TB diagnostic modalities were gathered. Patients were followed up to evaluate the occurrence of PRs, and cytokines IL2, IL6, IL18, and TNF alpha were analyzed using the sandwich ELISA principle at baseline and after PR development. Workflow of the study. Results Total 144 subjects with confirmed tuberculosis were recruited. PRs developed in 5.5% of patients, with fever (58.74%) and weight loss (44.06%) being the predominant systemic symptoms. The median time for PR development was 37 days, with pain and swelling being the most common presentation (62.5%). Among the baseline cytokines, IL6 was the most elevated (20.83%), with IL2, IL18, and TNF alpha being elevated in 8.3%, 0.69%, and 1.38% of the subjects, respectively. On multivariate analysis, baseline elevation of interleukin 2 was statistically significant and predicted PRs. IL2 and IL6 were significantly elevated during the occurrence of PRs, while IL18 and TNF alpha were not. Most patients (75%) improved on NSAIDs, with a median symptom resolution duration of 30 days. Comparison of patient parameters at baseline and after the development of paradoxical reactions. Comparison of cytokine levels at baseline and after paradoxical reactions. Paradoxical reaction features, tuberculosis diagnostic modalities and treatment modalities of paradoxical reaction. Conclusion Our study found that baseline elevation of IL-2 and worsening adenopathy and weight loss during treatment are potential predictors for paradoxical reaction in lymph-node tuberculosis. However, it is important to validate these findings through larger prospective studies. Disclosures All Authors: No reported disclosures

Background: The rapid and accurate diagnosis of tubercular lymphadenitis remains a challenging task today.WHO endorsed LoopAMP™ MTBC kit (TB-LAMP) as a replacement for sputum-smear microscopy in the diagnosis of pulmonary tuberculosis (PTB). However, no prospective diagnostic accuracy study of TB-LAMP in tubercular lymphadenitis in adults has been done yet. Current study evaluated the diagnostic performance of TB-LAMP in tubercular lymphadenitis (LNTB).Material & Methods: In a prospective observational study conducted at a tertiary care hospital in India, 90 subjects (age>18years) suspected of LNTB were consecutively recruited and followed up till six months between January 2019 and December 2020. Samples were processed for microscopy, culture, GeneXpert®, histopathology and TB-LAMP. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of TB-LAMP against composite reference standard (CRS) and culture were determined.Results : TB-LAMP showed a sensitivity of 83.78% (95% CI, 73.76-90.47) and specificity of 81.25% (95% CI, 56.99-93.41) respectively against CRS. The PPV and NPV were 95.38% (95% CI, 87.29-98.42) and 52.00% (95% CI, 33.50-69.97) respectively. TB-LAMP showed a sensitivity of 88.89% (95% CI, 71.94-96.15) and specificity of 36.17% (95% CI, 23.97-50.46) respectively against culture. The PPV and NPV were 44.44% (95% CI, 32-57.62) and 85% (95% CI, 63.96-94.76) respectively.Conclusion: TB-LAMP can be used over conventional microscopy for the diagnosis of TB in lymph node specimens at primary health care centres. This is the rapid and cost-effective diagnosis of LNTB in resource-limited settings due to good sensitivity and NPV.

Background The immunomodulatory effects of vitamin D are widely recognized and a few studies have been conducted to determine its utility in the treatment of tuberculosis, with mixed results. This study was conducted to see if vitamin D supplementation in patients with active pulmonary tuberculosis (PTB) in the Indian population contributed to sputum smear and culture conversion as well as the prevention of relapse. Methods This randomized double-blind placebo-controlled trial was conducted in three sites in India. HIV negative participants aged 15–60 years with sputum smear positive PTB were recruited according to the Revised National Tuberculosis Control Program guidelines and were randomly assigned (1:1) to receive standard anti-tubercular treatment (ATT) with either supplemental dose of oral vitamin D3 (60,000 IU/sachet weekly for first two months, fortnightly for next four months followed by monthly for the next 18 months) or placebo with same schedule. The primary outcome was relapse of PTB and secondary outcomes were time to conversion of sputum smear and sputum culture. Results A total of 846 participants were enrolled between February 1, 2017 to February 27, 2021, and randomly assigned to receive either 60,000 IU vitamin D3 (n = 424) or placebo (n = 422) along with standard ATT. Among the 697 who were cured of PTB, relapse occurred in 14 participants from the vitamin D group and 19 participants from the placebo group (hazard risk ratio 0.68, 95%CI 0.34 to 1.37, log rank p value 0.29). Similarly, no statistically significant difference was seen in time to sputum smear and sputum culture conversion between both groups. Five patients died each in vitamin D and placebo groups, but none of the deaths were attributable to the study intervention. Serum levels of vitamin D were significantly raised in the vitamin D group as compared to the placebo group, with other blood parameters not showing any significant difference between groups. Conclusions The study reveals that vitamin D supplementation does not seem to have any beneficial effect in the treatment of PTB in terms to the prevention of relapse and time to sputum smear and culture conversion. Trial registration CTRI/2021/02/030977 (ICMR, Clinical trial registry-India).

Purpose: Non-tuberculous Mycobacteria (NTM) infections are often misdiagnosed as tuberculosis due to the similar clinical and radiological presentations.NTM infections can be differentiated from tuberculosis only through species identification.Here we performed a species-level identification of NTM from sputum samples using ITS sequencing of the 16S-23S rRNA gene.Materials and Methods: Twenty-one immunochromatographic assay negative isolates from smear-positive patients were collected and evaluated.The isolates were then subjected to mycolic acid extraction for HPLC, DNA isolation for line probe assay (LPA), hsp65 and 16S-23S rRNA gene ITS sequencing. Results:After evaluating all the diagnostic modalities for NTM, it was observed that the Mycobacterium intracellulare was the predominant slow-growing NTM (9/20, 45%), while Mycobacterium abscessus (subsp.bolletii) was the dominant rapid grower (5/20, 25%).One isolate, which could not be identified either by LPA or by HPLC, was detected as Nocardia cyriacigeorgica, by sequencing a non mycobacterial species predominantly found in pulmonary infection.The results of HPLC and LPA were 100% concordant.One isolate was identified as M. abscessus by sequencing, but HPLC and LPA detected it as Mycobacterium chelonae. Conclusion:NTM should be considered as the key pathogen in immunocompromised patients and in patients with manifestations similar to tuberculosis.In such cases, species identification is critical for initiation of appropriate therapy.The 16S-23S rRNA gene ITS sequencing method is a rapid and accurate technique for NTM species identification up to subspecies.

Background The emergence of drug-resistant tuberculosis (TB), is a major menace to cast off TB worldwide. Line probe assay (LPA; GenoType MTBDRplus ver. 2) and Xpert MTB/RIF assays are two rapid molecular TB detection/diagnostic tests. To compare the performance of LPA and Xpert MTB/RIF assay for early diagnosis of rifampicin-resistant (RR) TB in acid-fast bacillus (AFB) smear-positive and negative sputum samples. Methods A total 576 presumptive AFB patients were selected and subjected to AFB microscopy, Xpert MTB/RIF assay and recent version of LPA (GenoType MTBDRplus assay version 2) tests directly on sputum samples. Results were compared with phenotypic culture and drug susceptibility testing (DST). DNA sequencing was performed with rpoB gene for samples with discordant rifampicin susceptibility results. Results Among culture-positive samples, Xpert MTB/RIF assay detected Mycobacterium tuberculosis (Mtb ) in 97.3% (364/374) of AFB smear-positive samples and 76.5% (13/17) among smear-negative samples, and the corresponding values for LPA test (valid results with Mtb control band) were 97.9% (366/374) and 58.8% (10/17), respectively. For detection of RR among Mtb positive molecular results, the sensitivity of Xpert MTB/RIF assay and LPA (after resolving discordant phenotypic DST results with DNA sequencing) were found to be 96% and 99%, respectively. Whereas, specificity of both test for detecting RR were found to be 99%. Conclusion We conclude that although Xpert MTB/RIF assay is comparatively superior to LPA in detecting Mtb among AFB smear-negative pulmonary TB. However, both tests are equally efficient in early diagnosis of AFB smear-positive presumptive RR-TB patients.

Microbiological diagnosis of extra-pulmonary tuberculosis (EPTB) has been one of the most difficult aspects of tuberculosis (TB) management. Availability of better imaging and diagnostic modalities has led to an increase in the number of diagnosed cases. The current upsurge in multidrug-resistant tuberculosis warrants routine testing of EPTB samples for resistance at baseline with shorter turn-around time. A total of 369 EPTB specimens were subjected to Ziehl-Neelsen (ZN) stain, liquid culture (LC) with phenotypic drug susceptibility testing, MTBDRplus V.2 and MTBDRsl V.2. The molecular categorisation of resistant specimens was further reconfirmed with sequencing. The sensitivity and specificity of MTBDRplus V.2 to detect Mycobacterium tuberculosis (MTB) when compared to ZN stain was 97.9% and 89.2%, respectively while it was 73.4% and 83.8%, respectively when compared to LC. Similarly, for MTBDRsl V.2, the sensitivity and specificity for detection of MTB when compared with ZN was 95.6% and 91.9%, respectively and 75% and 89.2%, respectively when compared to LC. In smear-positive specimens, 94% (141/150) and 86% (129/150) valid results were observed in MTBDRplus V.2 and MTBDRsl V.2, respectively. The utilisation of both MTBDRplus V.2 and MTBDRsl V.2 for the diagnosis of smear-positive EPTB specimens would be useful in programmatic management of TB in high-burden settings.

Background: Line probe assay (LPA) is standard diagnostic tool to detect multidrug resistant tuberculosis. Non-interpretable (NI) results in LPA (complete missing or light wild-type 3 and 8 bands with no mutation band in rpoB gene region) poses a diagnostic challenge. Methods: Sputum samples obtained between October 2016 and July 2017 at the Intermediate Reference Laboratory, All India Institute of Medical Sciences Hospital, New Delhi, India were screened. Smear-positive and smear-negative culture-positive specimens were subjected to LPA Genotype MTBDRplus Ver 2.0. Smear-negative with culture-negative and culture contamination were excluded. LPA NI samples were subjected to phenotypic drug susceptibility testing (pDST) using MGIT-960 and sequencing. Results: A total of 1,614 sputum specimens were screened and 1,340 were included for the study (smear-positive [n=1,188] and smear-negative culture-positive [n=152]). LPA demonstrated 1,306 (97.5%) valid results with TUB (Mycobacterium tuberculosis) band, 24 (1.8%) NI, three (0.2%) valid results without TUB band, and seven (0.5%) invalid results. Among the NI results, 22 isolates (91.7%) were found to be rifampicin (RIF) resistant and two (8.3%) were RIF sensitive in the pDST. Sequencing revealed that rpoB mutations were noted in all 22 cases with RIF resistance, whereas the remaining two cases had wild-type strains. Of the 22 cases with rpoB mutations, the most frequent mutation was S531W (n=10, 45.5%), followed by S531F (n=6, 27.2%), L530P (n=2, 9.1%), A532V (n=2, 9.1%), and L533P (n=2, 9.1%). Conclusion: The present study showed that the results of the Genotype MTBDRplus assay were NI in a small proportion of isolates. pDST and rpoB sequencing were useful in elucidating the cause and clinical meaning of the NI results.

Background: The treatment of drug-resistant tuberculosis (TB) involves various regimens. Among them, the most promising antibiotic regimens are fluoroquinolone (FQ) drugs. Drug susceptibility testing (DST) for FQs is not included as routine assessment for baseline TB diagnosis. Limited resources are available about FQ resistance among extrapulmonary TB (EPTB) cases. Methods: A total of 447 culture-positive specimens were subjected to DST for first-line anti-TB drugs (FLDs) and second-line anti-TB drugs. DST was performed using automated mycobacterium growth indicator tube-960 liquid culture techniques. The study was carried out during the period of April 2016 to March 2017. In addition, DST of FQs was also performed in FLD-sensitive strains. Results: Mycobacterium tuberculosis was isolated from 447 specimens. Of the 447 culture-positive EPTB specimens, 54 were rifampicin-resistant (RR)/multidrug-resistant TB (MDR-TB) isolates, 45 isolates were resistant to any drug, and the remaining 348 were sensitive to FLDs. Monoresistance of FQs was observed in 20.4% (11/54) among RR/MDR-TB isolates and 4.3% (15/348) among FLD-sensitive isolates. Conclusion: The high degree of FQ resistance observed in EPTB specimens among drug-sensitive and MDR-TB isolates is alarming. This study reflects the need to expand culture and DST for EPTB cases and include FQs within first-line DST in such settings. Furthermore, there should be a rational use of FQs for the treatment of other diseases.

Background & objectives: Nasopharyngeal and oropharyngeal swab (NPS and OPS) collection is widely accepted as the preferred method for obtaining respiratory samples. However, it has certain disadvantages which may be overcome by gargling. The primary objective of this study was to assess agreement between gargle lavage and swab as an appropriate respiratory sample for the detection of SARS-CoV-2. The secondary objective was to assess the patient acceptability of the two sampling methods. Methods: It was a cross-sectional study done at a tertiary care hospital in New Delhi, India, on 50 confirmed COVID-19 patients. Paired swab (NPS and OPS) and gargle samples were taken within 72 h of their diagnosis. Samples were processed by reverse transcription-polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2. Post-sample collection, a 10-point scale was administered to assess the level of discomfort with either of the collection methods. Results: All gargle samples were positive and comparable to their corresponding swab samples irrespective of the symptoms and duration of illness. The cycle threshold (Ct) values for gargle samples were slightly higher but comparable to those of swabs. Bland-Altman plot showed good agreement between the two methods. Majority (72%) of the patients reported moderate-to-severe discomfort with swab collection in comparison to 24 per cent reporting only mild discomfort with gargle collection. Interpretation & conclusions: Our preliminary results show that the gargle lavage may be a viable alternative to swabs for sample collection for the detection of SARS-CoV-2. Adoption of gargle lavage for sample collection will have a significant impact as it will enable easy self-collection, relieve healthcare workers and also lead to substantial cost savings by reducing the need for swabs and personal protective equipment.

Background:Mutations in atpE gene or transcriptional repressor Rv0678 gene associated with inhibition of adenosine 5'-triphosphate synthase and upregulation of efflux pumps, respectively, may potentially lead to in vitro resistance to bedaquiline. This is the first study from India, which looks at mutations associated with this novel drug. Methods:In 2019 (January to June), a total of 68 laboratory-confirmed pre-extensively drug-resistant tuberculosis (XDR-TB) (fluoroquinolone resistant [n = 52] and second-line injectables resistant [n = 12]) and 4 × DR-TB culture specimens were included. All specimens were evaluated for genetic analysis using predesigned primers of atpE and Rv0678 genes. Results:Among the pre-XDR-TB isolates (n = 64), there were no mutations found in either atpE or Rv0678. However, among the XDR-TB isolates (n = 4), one specimen (25%) was found to be associated with a mutation in atpE gene at position 49, resulting in the amino acid leucine replaced by proline (L-49-P). No mutations were observed with the Rv0678 gene. Conclusion:In this study, genetic analysis showed that only one-fourth XDR-TB isolates had a mutation in the atpE gene; there were no other mutations found in the Rv0678 gene. To the best of our knowledge, this novel mutation (L-49-P) in atpE gene is being reported for the first time in northern India.

CONTEXT:Nontuberculous mycobacteria (NTM) are ubiquitous mycobacteria present in environment and generally affect patients with either structural lung disease or immunosuppression and commonly involve lungs, lymph node, or skin.MATERIALS AND METHODS:Between July 2016 and February 2019, 18 cases of NTM were diagnosed and their relevant clinical, diagnostic, and treatment details were recorded after taking informed consent.RESULTS:We report 18 cases of NTM involving lungs (n = 11), skin and soft tissue (n = 3), joint (n = 2), genitourinary (n = 1), and central nervous system (n = 1). History of immunosuppression was present in two patients, whereas history of some form of intervention was seen in six patients. Mycobacterium fortuitum group (n = 5) was the most commonly isolated organism, followed by Mycobacterium avium complex (n = 4), Mycobacterium abscessus (n = 3), Mycobacterium kansasii (n = 2), and Mycobacterium chelonae (n = 1). In two patients, M. chelonae and M. abscessus were isolated in succession. Of these 18 patients, clinical response was present in 15 of the patients. Diagnosis and treatment of NTM in resource limited settings is extremely challenging.CONCLUSION:Most of the patients with NTM are misdiagnosed and are treated as tuberculosis in India, sometimes with a multidrug resistance regimen, which results in significant morbidity and mortality. We present these cases to shed some light on the epidemiology of NTM in this part of India.

Laparoscopic port-site infections, though infrequent, undermine the advantages provided by minimally invasive surgeries. Persistent nonhealing discharging sinuses, not responding to conventional antibiotic therapy, pose diagnostic and therapeutic challenges. Sizeable number of these infections is caused by rapidly growing nontuberculous mycobacteria (NTM), and diagnosing these requires a high index of suspicion. We present a case of a nonhealing laparoscopic cholecystectomy umbilical port-site infection caused by Mycobacterium senegalense, a rare NTM. The patient recovered completely after 6 months of combination therapy with clarithromycin, trimethoprim-sulfamethoxazole, and levofloxacin.

The management of neurological infections due to non-tubercular mycobacteria is extremely challenging because of scarce literature, issues with penetration, lack of easily available susceptibility platforms and adverse effects associated with long term therapy. We report a case of a young girl with neurological infection due to rapidly growing mycobacteria to discuss the factors that should be considered while choosing the therapy for such rare and persistent infections.

Extensively drug‐resistant tuberculosis (XDR‐TB) is defined as a strain of Mycobacterium tuberculosis that is resistant to isoniazid, rifampicin, any one of the fluoroquinolones and any one of the aminoglycosides.[1] Although nomograms for predicting drug resistant tuberculosis has been suggested in recent times, the diagnosis of XDR TB is mostly microbiological.[2] The standardized treatment regimen of XDR‐TB in India before 2017 consisted of 6‐12 months of intensive phase therapy (capreomycin, moxifloxacin, high dose isoniazid, para‐aminosalicylic acid, clofazimine, linezolid, and amoxicillin‐clavulanate) followed by 18 months of continuation phase therapy (all except capreomycin). This study aimed to delineate the epidemiology of XDR‐TB and outcomes associated with the long‐term standardized treatment regimen.