About

Padmapriya P. Banada, PHD, MS, is an Associate Professor-Research in the Department of Medicine at Rutgers New Jersey Medical School. She obtained her PhD from Mysore University, India, where she developed molecular methods for detecting enterotoxigenic staphylococci and applied these in food quality programs. She further worked as a postdoctoral research associate at Purdue University in Bhunia lab, focusing on molecular diagnostics, immunoassays, cytotoxicity assays, lab-on-chip diagnostics, and optical light scattering technology. Dr. Banada joined New Jersey Medical School as a research scientist, collaborating with Dr. David Alland, and contributed significantly to the development of the Xpert MTB/RIF assay and the Xpert MTB ultra. She developed novel sample processing methods for blood and stool samples to detect tuberculosis in immunocompromised patients and children. Her current research projects involve the development of advanced diagnostics in bio-defense and sepsis, with a focus on fungal sepsis and hemorrhagic fever viruses, including Ebola virus. With over 15 years of experience in molecular diagnostics of infectious diseases and tuberculosis, she has received multiple awards, holds five US and European patents, and has published extensively in peer-reviewed journals.

Research topics

• Medicine
• Virology
• Biology
• Internal medicine
• Genetics
• Molecular biology
• Microbiology

Selected publications

• A streamlined CRISPR-based test for tuberculosis detection directly from sputum

  Science Advances · 2025-08-06 · 19 citations

  articleOpen access

  Mycobacterium tuberculosis ( Mtb ) is a major threat to global health, and there is an urgent need for affordable, simple tuberculosis (TB) diagnosis in underresourced areas. Here, we combine recombinase polymerase amplification with Cas13a and Cas12a detection to create two parallelized one-pot assays that detect two conserved elements of Mtb ( IS6110 and IS1081 ) and a human DNA internal control. These assays are compatible with lateral flow and can be readily lyophilized. Our final assay showed a limit of detection of 69.0 CFU per milliliter for Mtb H37Rv and 80.5 CFU per milliliter for Mycobacterium bovis BCG in spiked sputum, with no cross-reactivity to diverse bacterial or fungal isolates. Clinical tests on 13 blinded sputum samples revealed 100% (six of six) sensitivity and 100% (seven of seven) specificity compared to culture. SHINE-TB streamlines TB diagnosis from sample to answer by combining amplification and detection while being compatible with lateral flow and lyophilization.

  PublisherDOI

• Prominence of Mycobacterium tuberculosis biomarkers among sputum culture-negative clinic attendees, independent of Ultra status

  Journal of Infection and Public Health · 2025-04-24 · 3 citations

  articleOpen access

  BACKGROUND: Highly-sensitive molecular tests like GeneXpert MTB/RIF Ultra improve detection of paucibacillary pulmonary tuberculosis (TB) but occasionally detect Mycobacterium tuberculosis (Mtb) DNA in sputum from culture-negative individuals, with unclear significance. We hypothesized that Ultra may be detecting culture-negative TB, and manifest in a higher prevalence of TB biomarkers compared to Ultra-negative/culture-negative ('sputum-negative') individuals. METHODS: From 1200 symptomatic African adults undergoing evaluation for TB, we identified 66 with discordant results (Ultra-positive, culture-negative), and matched 52 sputum-negative (Ultra-negative, culture-negative) and 30 sputum-positive (Ultra-positive, culture-positive) participants. Over 12 months, participants were assessed for Mtb biomarkers (Mtb growth in augmented or follow-up sputum cultures, Mtb mRNA in baseline sputum, and symptomatic Ultra-positive after baseline) and TB-associated host transcriptional signatures. RESULTS: At baseline, TB-associated biomarker(s) were detected in 51.5 % of sputum-discordant versus 59.6 % of sputum-negative participants (p = 0.46), with at least one Mtb biomarker in 16.7 % versus 26.9 % respectively (p = 0.26). Longitudinally, 26.5 % of untreated sputum-discordant versus 41.7 % of untreated sputum-negative participants had Mtb biomarkers (p = 0.17) despite most reporting symptom improvement. Notably, 30 % of untreated sputum-negative participants converted to Ultra-positive at month 2. One sputum-discordant and one sputum-negative participant developed culture-confirmed TB at follow-up. CONCLUSION: TB bacterial and host biomarkers were prevalent and no different between sputum-discordant and sputum-negative participants, raising concern for a considerable population of undiagnosed culture-negative TB. These findings parallel new evidence of Mtb aerosolization from sputum-negative individuals and highlight a need for more comprehensive diagnostics that detect sputum culture-negative TB with respect to infectiousness, pathology, and risk of progression.

  PublisherDOI

• Optimal processing of tongue swab samples for <i>Mycobacterium tuberculosis</i> detection by the Xpert MTB/RIF Ultra assay

  Microbiology Spectrum · 2025-01-28 · 7 citations

  articleOpen access

  ABSTRACT Tongue swabs represent a potential alternative to sputum as a sample type for detecting pulmonary tuberculosis (TB) with molecular diagnostic tests. The methods used to process tongue swabs for testing in the World Health Organization-recommended Xpert MTB/RIF Ultra (Xpert Ultra) assay vary greatly. Here, we aimed to identify the optimal tongue swab processing for Xpert Ultra testing. We compared four methods for treating dry tongue swabs with the Xpert Sample Reagent (SR) mixed with various concentrations of Tris–EDTA–Tween to treatment with SR alone or to a commonly used heat inactivation protocol. In each condition, swabs obtained from volunteers without TB were placed into test buffer spiked with known amounts of Mycobacterium tuberculosis ( Mtb ) H37Rv-mc 2 6230. Swabs processed with 1:1 diluted SR buffer had the lowest Mtb limit of detection (LOD) at 22.7 CFU/700 µL (95% confidence interval (CI) 14.2–31.2), followed by 2:1 diluted SR buffer at 30.3 CFU/700 µL (95% CI 19.9–40.7), neat SR at 30.9 CFU/700 µL (95% CI 21.5–40.3), and SR prefilled in the Xpert Ultra at 57.1 CFU/700 µL (95% CI 42.4–71.7). Swabs processed using the heat-based protocol had the highest LOD (77.6 CFU/700 µL; 95% CI 51.2–104.0). Similar findings were observed for the LOD of RIF susceptibility. The 2:1 diluted SR buffer condition produced similar LODs when swabs were tested in the presence of sputum matrix or phosphate buffer saline. Further studies are needed to assess the performance of this processing protocol in a clinical setting. IMPORTANCE Xpert MTB/RIF Ultra (Xpert Ultra) is approved by the World Health Organization for the diagnosis of tuberculosis (TB). This test is typically performed using sputum specimens obtained from people with presumptive TB. In order to inactivate Mycobacterium tuberculosis ( Mtb ) and aid liquefaction, sputum must be mixed with Xpert SR prior to transfer into the Xpert Ultra. However, some people under evaluation for TB are unable to produce sputum. Alternative sample types for TB diagnosis would, therefore, be of value. Oral swabs, including tongue swabs, have shown promise, but there are technical challenges associated with sample processing. In this study, several new tongue swab processing conditions were evaluated by utilizing SR, either neat or diluted in buffer. The ability of Xpert Ultra to detect TB was improved under these conditions compared with the previously published heat-processing method; processing steps were simplified; and technical challenges were overcome.

  PublisherDOI

• Simplified Co-extraction of total Nucleic Acids from Respiratory Samples for detection of <i>Mycobacterium tuberculosis</i> and SARS-CoV-2 optimized for compatibility across Diagnostic Platforms

  medRxiv · 2025-03-03 · 3 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Tuberculosis (TB) and COVID-19 are leading infectious diseases with high mortality, caused by Mycobacterium tuberculosis ( Mtb ) and SARS-CoV-2 (SC2) , respectively. Co-infection is common but is often undiagnosed as it is challenging to process both pathogens from a single sample. In this study, we present a simple and efficient method for co-extracting nucleic acids (NA) from these two distinct respiratory pathogens for downstream diagnostic testing. We evaluated three different nucleic acid amplification (NAA)-based platforms, LightCycler480 (LC480) qPCR, Qiacuity digital PCR (dPCR), and Cytation3 for CRISPR-Cas13a-based SHINE-TB/SC2 detection assays. Chelex-100 chelating resin-based boiling preparation method was optimized for Mtb NA extraction from saliva and sputum. Saliva showed compatibility with all three platforms, with sensitivity as low as 100 CFU/ml (or 2 genomic copies/µl). This method worked well for sputum using dPCR at 100% (21/21) positivity, though the CRISPR-based SHINE-TB assay showed more variability and sensitivity to sputum inhibitor carry-over, resulting in an 81% positive rate (17/21). Diluting sputum with TE buffer (1:1) improved the detection (2/4). Extraction efficiency of our method was 48%, 62.2%, 86.4% and 99.3% for concentrations 10 5 , 10 4 , 10 3 and 10 CFU/ml, respectively. The dynamic range for Mtb spiked in pooled sputum showed 100% detection (N=8) at ≥10 3 CFU/ml with all three methods. Dual-pathogen co-extraction and detection of SC2 (10 5 PFU/ml) and Mtb (10 5 CFU/ml) in salivary sputum was successful using CRISPR-Cas13a assays. We have developed a rapid and efficient co-extraction method for multi-pathogen testing across diagnostic platforms and believe this is the first protocol optimized to co-extract Mtb and SARS-CoV-2 from a single sample.

  PublisherOA PDFDOI

• A Streamlined Point-of-Care CRISPR Test for Tuberculosis Detection Directly from Sputum

  medRxiv · 2025-02-21

  preprintOpen access

  Abstract Mycobacterium tuberculosis ( Mtb ) is a major threat to global health and is responsible for over one million deaths each year. To stem the tide of cases and maximize opportunities for early interventions, there is an urgent need for affordable and simple means of tuberculosis diagnosis in under-resourced areas. We sought to develop a CRISPR-based isothermal assay coupled with a compatible, straightforward sample processing technique for point-of-care use. Here, we combine Recombinase Polymerase Amplification (RPA) with Cas13a and Cas12a, to create two parallelised one-pot assays that detect two conserved elements of Mtb ( IS6110 and IS1081 ) and an internal control targeting human DNA. These assays were shown to be compatible with lateral flow and can be readily lyophilized. Our finalized assay exhibited sensitivity over a wide range of bacterial loads (10 5 to 10 2 CFU/mL) in sputum. The limit of detection (LoD) of the assay was determined to be 69.0 (51.0 – 86.9) CFU/mL for Mtb strain H37Rv spiked in sputum and 80.5 (59.4 – 101.6) CFU/mL for M. bovis BCG. Our assay showed no cross reactivity against a wide range of bacterial/fungal isolates. Clinical tests on 13 blinded sputum samples revealed 100% (6/6) sensitivity and 100% (7/7) specificity compared to culture. Our assay exhibited comparable sensitivity in clinical samples to the microbiological gold standard, TB culture, and to the nucleic acid state-of-the-art, GeneXpert MTB/RIF Ultra. This technology streamlines TB diagnosis from sample extraction to assay readout in a rapid and robust format, making it the first test to combine amplification and detection while being compatible with both lateral flow and lyophilization.

  PublisherOA PDFDOI

• Stool Processing Methods for Xpert Ultra Testing in Childhood Tuberculosis: A Prospective, Multicountry Accuracy Study

  Clinical Infectious Diseases · 2025-05-31 · 2 citations

  articleOpen access

  BACKGROUND: Centrifuge-free processing methods support stool Xpert Ultra testing for childhood tuberculosis, but data on their accuracy, acceptability, and usability are limited. METHODS: We conducted a prospective evaluation of stool Xpert Ultra in India, South Africa, and Uganda with 3 methods: the Stool Processing Kit (SPK), the Simple One-Step method (SOS), and the Optimized Sucrose Flotation method (OSF). Children <15 years old with presumptive tuberculosis underwent sputum testing with Xpert Ultra and culture. We compared the accuracy of each method against a microbiological reference standard (tuberculosis if Xpert Ultra or culture positive) and a composite reference standard (tuberculosis if confirmed or unconfirmed tuberculosis). We surveyed laboratory staff to assess the acceptability and usability of the methods. RESULTS: We included 607 children, with a median age of 3.5 years (interquartile range, 1.3-7 years); 15.5% were human immunodeficiency virus positive. Against the microbiological reference standard, the sensitivities of SPK, SOS, and OSF were 36.9% (95% confidence interval, 28.6%-45.8%), 38.6% (17.2%-51.0%), and 31.3% (20.2%-44.1%), respectively, and the specificities, 98.2% (96.4%-99.3%), 97.3% (93.7%-99.1%), and 97.1% (93.3%-99%). The methods were acceptable and usable, but SOS was reported as most feasible to implement in a peripheral facility. Across methods, sensitivities increased among children who were culture positive (range, 55.0%-77.3%) and were low (13%-16.7%) against the composite reference standard. Adding stool Xpert Ultra increased sensitivity from 0% (OSF) to 11.8% (SPK/SOS), compared with sputum alone. CONCLUSIONS: Stool processing methods for Xpert Ultra were acceptable and usable and performed similarly, with highest sensitivity among children with culture-positive tuberculosis.

  PublisherOA PDFDOI

• A simple and sensitive test for <i>Candida auris</i> colonization, surveillance, and infection control suitable for near patient use

  Journal of Clinical Microbiology · 2024-06-18 · 4 citations

  articleOpen accessSenior author

  ABSTRACT Candida auris is a multidrug-resistant fungal pathogen with a propensity to colonize humans and persist on environmental surfaces. C. auris invasive fungal disease is being increasingly identified in acute and long-term care settings. We have developed a prototype cartridge-based C. auris surveillance assay (CaurisSurV cartridge; “research use only”) that includes integrated sample processing and nucleic acid amplification to detect C. auris from surveillance skin swabs in the GeneXpert instrument and is designed for point-of-care use. The assay limit of detection (LoD) in the skin swab matrix was 10.5 and 14.8 CFU/mL for non-aggregative (AR0388) and aggregative (AR0382) strains of C. auris , respectively. All five known clades of C. auris were detected at 2-3-5× (31.5–52.5 CFU/mL) the LoD. The assay was validated using a total of 85 clinical swab samples banked at two different institutions (University of California Los Angeles, CA and Wadsworth Center, NY). Compared to culture, sensitivity was 96.8% (30/31) and 100% (10/10) in the UCLA and Wadsworth cohorts, respectively, providing a combined sensitivity of 97.5% (40/41), and compared to PCR, the combined sensitivity was 92% (46/50). Specificity was 100% with both clinical ( C. auris negative matrix, N = 31) and analytical (non- C . auris strains, N = 32) samples. An additional blinded study with N = 60 samples from Wadsworth Center, NY yielded 97% (29/30) sensitivity and 100% (28/28) specificity. We have developed a completely integrated, sensitive, specific, and 58-min prototype test, which can be used for routine surveillance of C. auris and might help prevent colonization and outbreaks in acute and chronic healthcare settings. IMPORTANCE This study has the potential to offer a better solution to healthcare providers at hospitals and long-term care facilities in their ongoing efforts for effective and timely control of Candida auris infection and hence quicker response for any potential future outbreaks.

  PublisherOA PDFDOI

• Stool processing methods for Xpert Ultra testing in childhood tuberculosis: A prospective, multi-country accuracy study

  medRxiv · 2024-12-19 · 2 citations

  preprintOpen access

  Background: Centrifuge-free processing methods support stool Xpert Ultra testing for childhood tuberculosis (TB), but there are limited data on their accuracy, acceptability and usability. Methods: We conducted a prospective evaluation of stool Xpert Ultra in India, South Africa, and Uganda with three methods: Stool Processing Kit (SPK), Simple One-Step (SOS), and Optimized Sucrose Flotation (OSF). Children <15 years old with presumptive TB had respiratory specimen testing with Xpert Ultra and culture. Stool was tested using Xpert Ultra after processing with each method. We compared the accuracy of each method to a microbiological reference standard (MRS) and a composite reference standard (CRS). We surveyed the laboratory staff to assess acceptability and usability of the methods. Results: We included 607 children, of whom the median age was 3.5 years (IQR 1.3-7), 48% were female, and 15.5% were HIV positive. Against the MRS, the sensitivities of SPK, SOS and OSF were 36.9% (95% CI 28.6-45.8), 38.6% (95% CI 17.2-51), and 31.3% (95% CI 20.2-44.1), respectively. The specificities of SPK, SOS and OSF were 98.2% (95% CI 96.4-99.3), 97.3% (95% CI 93.7-99.1) and 97.1% (95% CI 93.3-99), respectively. Laboratory staff reported that the methods were acceptable and usable, but SOS was most feasible to implement in a peripheral facility. Sensitivity increased among children who were culture-positive (55-77.3%) and was low (13-16.7%) against the CRS. Conclusions: Stool processing methods for Xpert Ultra were acceptable, usable, and performed similarly, with highest sensitivity among children with culture-positive TB.

  PublisherOA PDFDOI

• Optimal processing of tongue swab samples for Mycobacterium tuberculosis detection by the Xpert MTB/RIF Ultra assay

  medRxiv · 2024-06-22 · 1 citations

  preprintOpen access

  Abstract Tongue swabs represent a potential alternative to sputum as a sample type for detecting pulmonary tuberculosis (TB) using molecular diagnostic tests. The methods used to process tongue swabs for testing in the WHO-recommended Xpert MTB/RIF Ultra (Xpert Ultra) assay vary greatly. We aimed to identify the optimal method for processing diagnostic tongue swabs for subsequent testing by Xpert Ultra. We compared four methods for treating dry tongue swabs with Xpert Ultra sample reagent (SR) mixed with various concentrations of Tris-EDTA-Tween (TET), to treatment with SR alone or to a commonly used SR-free heat-inactivation protocol. In each condition, swabs obtained from volunteers without TB were placed into test buffer spiked with known amounts of Mycobacterium tuberculosis ( Mtb ) strain H37Rv-mc 2 6230. Swabs processed with 1:1 diluted SR buffer had the lowest Mtb limit of detection (LOD) at 22.7 CFU/700 µl (95% CI 14.2-31.2), followed by 2:1 diluted SR buffer at 30.3 CFU/700 µl (95% CI 19.9-40.7), neat SR at 30.9 CFU/700 µl (95% CI 21.5-40.3) and SR prefilled in the Xpert Ultra at 57.1 CFU/700 µl (95% CI 42.4-71.7). Swabs processed using the heat-based protocol had the highest LOD (77.6 CFU/700 µl; 95% CI 51.2–104.0). Similar findings were observed for LOD of RIF-susceptibility. Assay sensitivity using the 2:1 diluted SR buffer did not vary considerably in the presence of sputum matrix or phosphate buffer saline. Further studies are needed to assess the performance of this processing protocol in a clinical setting. Importance Xpert MTB/RIF Ultra (Xpert Ultra) is approved by the World Health Organization for the diagnosis of tuberculosis (TB). This test is typically performed using sputum specimens obtained from people with presumptive TB. In order to inactivate Mtb and aid liquefaction, sputum must be mixed with Xpert SR prior to transfer into the Xpert Ultra. However, some people under evaluation for TB are unable to produce sputum. Alternative sample types for TB diagnosis would therefore be of value. Oral-swabs, including tongue-swabs have shown promise, but there are technical challenges associated with sample processing. In this study, several new tongue swab processing conditions were evaluated, utilizing SR, either neat or diluted in buffer. The ability of Xpert Ultra to detect TB was improved under these conditions compared with the previously published heat-processing method (1–3), processing steps were simplified, and technical challenges were overcome.

  PublisherOA PDFDOI

• An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

  Scientific Reports · 2023-12-11 · 8 citations

  articleOpen access1st authorCorresponding

  The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.

  PublisherOA PDFDOI

Frequent coauthors

• David Alland

  Rutgers, The State University of New Jersey

  112 shared

• Soumitesh Chakravorty

  49 shared

• Sukalyani Banik

  Rutgers, The State University of New Jersey

  37 shared

• Arun K. Bhunia

  33 shared

• Naranjargal Daivaa

  Rutgers New Jersey Medical School

  20 shared

• Yingda L. Xie

  19 shared

• Abby Chopoorian

  Rutgers, The State University of New Jersey

  17 shared

• Rashid Bashir

  University of Illinois Urbana-Champaign

  17 shared

Education

• Ph.D.

  Mysore University

  2004

• M.S.

  Bangalore University, India

  1997

• B.S.

  Bangalore University, India

  1995

Awards & honors

• Purdue Agriculture team award