Sneha Chunchanur

Bangalore Medical College and Research Institute

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R. Ambica

Bangalore Medical College and Research Institute

Ambica Rangaiah

Bangalore Medical College and Research Institute

Shwetha Venugopal

Bangalore Medical College and Research Institute

Sarita Mohapatra

All India Institute of Medical Sciences

Nagasuma Chandra

Indian Institute of Science Bangalore

Ushashi Banerjee

Indian Institute of Science Bangalore

Vibhor Tak

All India Institute of Medical Sciences Jodhpur

Pankaj Hari

All India Institute of Medical Sciences

Pritik A Shah

Bangalore Medical College and Research Institute

Sathyanarayan Muthur Shankar

Bangalore Medical College and Research Institute

Cooperative Institutions

Areté Associates (United States)

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All India Institute of Medical Sciences

Cooley (United States)

Bangalore Medical College and Research Institute

University of Saint Mary of the Lake

Walter Eucken Institut

Carrington College

All India Institute of Medical Sciences Raipur

All India Institute of Medical Sciences Bhopal

Itron (France)

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GENOMIC DATA SETS DESCRIBING GENETIC BACKGROUND AND CIRCULATING LINEAGES OF NEISSERIA GONORRHOEAE IN BANGALORE, INDIA

International Journal of Infectious Diseases (2023)

N. Geetha J. V. Shwetha Sneha Chunchanur Varun Shamanna M. Bhaskaran

Neisseria gonorrhoeae

Neisseria

10.1016/j.ijid.2023.04.212

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Significance of isolation and drug susceptibility testing of non-Candida albicans species causing oropharyngeal candidiasis in HIV patients.

PubMed (2008)

Shobha D. Nadagir Sneha Chunchanur L. H. Halesh K. Yasmeen M R Chandrasekhar

Oropharyngeal candidiasis (OPC) continues to be a common opportunistic infection in patients infected with Human Immunodeficiency Virus (HIV) and is predictive of increasing immunosuppression. Though Candida albicans remains the predominant isolate, a rise in the frequency of isolation of non-albicans Candida (NAC) species is being observed. The levels of virulence and the sensitivities to available antifungal drugs vary among these species. Of 340 HIV seropositive patients in this study, 132 (38.8%) had oral lesions suggestive of candidiasis. Samples were collected from the lesion using sterile cotton swabs. Isolation and speciation were done by standard techniques. Antifungal drug susceptibility testing was done by macro broth dilution. The total number of Candida isolates was 135, of which, 45 (33.3%) were NAC species and 90 were C.albicans (66.6%). Of the NAC species, C. dubliniensis was the predominant pathogen (22,48.9%). Antifungal susceptibility testing showed that 14 (31.1%) of the NAC species and 11 (12.2%) of C. albicans were resistant to fluconazole (MIC > 8 microg/ml). A very high MIC of > 32 microg/ml was noted among the NAC species resistant to fluconazole.

Candida dubliniensis

Isolation

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Culture-Independent Raman Spectroscopic Identification of Bacterial Pathogens from Clinical Samples Using Deep Transfer Learning

Analytical Chemistry (2022)

Saumya Singh Dipak Kumbhar Dhanya Reghu Shwetha Venugopal P. T. Rekha

The rapid identification of bacterial pathogens in clinical samples like blood, urine, pus, and sputum is the need of the hour. Conventional bacterial identification methods like culturing and nucleic acid-based amplification have limitations like poor sensitivity, high cost, slow turnaround time, etc. Raman spectroscopy, a label-free and noninvasive technique, has overcome these drawbacks by providing rapid biochemical signatures from a single bacterium. Raman spectroscopy combined with chemometric methods has been used effectively to identify pathogens. However, a robust approach is needed to utilize Raman features for accurate classification while dealing with complex data sets such as spectra obtained from clinical isolates, showing high sample-to-sample heterogeneity. In this study, we have used Raman spectroscopy-based identification of pathogens from clinical isolates using a deep transfer learning approach at the single-cell level resolution. We have used the data-augmentation method to increase the volume of spectra needed for deep-learning analysis. Our ResNet model could specifically extract the spectral features of eight different pathogenic bacterial species with a 99.99% classification accuracy. The robustness of our model was validated on a set of blinded data sets, a mix of cultured and noncultured bacterial isolates of various origins and types. Our proposed ResNet model efficiently identified the pathogens from the blinded data set with high accuracy, providing a robust and rapid bacterial identification platform for clinical microbiology.

10.1021/acs.analchem.2c03391

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Detection and antifungal susceptibility testing of oral Candida dubliniensis from human immunodeficiency virus-infected patients

Indian Journal of Pathology and Microbiology (2009)

Sneha Chunchanur ShobhaD Nadgir L. H. Halesh BS Patil Yasmeen Kausar

Context: Candida dubliniensis, an opportunistic yeast that has been implicated in oropharyngeal candidiasis (OPC) in patients infected with Human Immunodeficiency Virus (HIV) may be under-reported due to its similarity with Candida albicans. Resistance to Fluconazole is often seen in C. dubliniensis isolates from clinical specimens. Aims: To know the prevalence of C. dubliniensis in OPC in patients infected with HIV and their antifungal susceptibility pattern. Settings and Design: One hundred and thirty-two HIV seropositive individuals and 50 healthy controls were included in the study. Materials and Methods: Two oral swabs were collected from the site of the lesion from 132 HIV-infected patients. Oral rinse was obtained from 50 healthy controls. Samples were inoculated on Sabouraud's dextrose agar (SDA) medium and on HiCrome Candida Differential Agar (CHROM agar) medium. Isolates were speciated by standard tests. Dark green-colored, germ tube positive isolates, which failed to grow at 420C and negative for xylose assimilation were identified as
C. dubliniensis. Antifungal susceptibility test was performed by Macro broth dilution technique (National Committee for Clinical Laboratory Standards guidelines). Results and Conclusions: From 132 patients, 22 (16.3%) C. dubliniensis were isolated; samples from healthy controls did not reveal their presence. Antifungal susceptibility test showed higher resistance among C. dubliniensis isolates to azoles compared to C. albicans. Five (22.7%) isolates of C. dubliniensis were resistant to Fluconazole followed by four (18.2%) to Ketoconazole. This study emphasizes the importance of identification and antifungal susceptibility testing of C. dubliniensis in HIV-infected patients.

Candida dubliniensis

Germ tube

Agar dilution

10.4103/0377-4929.56138

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Systems-level profiling of early peripheral host-response landscape variations across COVID-19 severity states in an Indian cohort

Genes and Immunity (2023)

Ushashi Banerjee Sneha Chunchanur R. Ambica Kithiganahalli Narayanaswamy Balaji Amit Singh

10.1038/s41435-023-00210-1

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Outbreak of Pichia kudriavzevii fungaemia in a neonatal intensive care unit

Journal of Medical Microbiology (2017)

T Nagarathnamma Sneha Chunchanur Shivaprakash M. Rudramurthy K. R. Vineetha Karthik Ramamurthy

Fungaemia is associated with substantial morbidity and mortality in neonates admitted to neonatal intensive care units (NICUs). We report an outbreak of fungaemia in a NICU due to rare yeast, Pichia kudriavzevii (a teleomorph of Candida krusei). To the best of our knowledge, this is the first report of neonatal sepsis due to P. kudriavzevii.Between August and September 2014, blood cultures from nine neonates diagnosed with late-onset sepsis in the NICU yielded yeast-like organisms. The molecular identification and typing of these isolates was performed by sequencing the D1/D2 region of 26S rDNA and fluorescent amplified fragment length polymorphism (FAFLP) respectively. Antifungal susceptibility was tested by broth microdilution as per the Clinical Laboratory Standards Institute (CLSI) guidelines. Sampling from environmental sources and the hands of healthcare workers (HCWs) in the NICU was performed.Of the nine neonates, eight were preterm and six had very low birth weight (VLBW). Thrombocytopenia was present in two neonates. Sequencing identified all the isolates as P. kudriavzevii and FAFLP showed their clonal origin. Antifungal susceptibility testing revealed the susceptibility of all isolates to the antifungals tested. Treatment with voriconazole was advised. However, only seven neonates were treated successfully and discharged after improvement, whereas two were lost for follow-up. Cultures from the environment and the hands of HCWs were negative. The outbreak was controlled by the strict implementation of infection control practices.This study emphasizes the importance of accurate identification of the aetiological agent of sepsis and vigilant monitoring for the possibility of an outbreak in NICUs.

Fungemia

10.1099/jmm.0.000645

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Diagnosis of Rickettsioses in Clinically Suspected Cases of Rickettsial Fever by Real-Time PCR in a Tertiary Care Centre

SSR Institute of International Journal of Life Sciences (2024)

Ashish Anshuman Ambica Rangaiah Sneha Chunchanur Shwetha Venugopal

Tertiary care

10.21276/ssr-iijls.2024.10.5.13

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Pressured cytotoxic T cell epitope strength among SARS‐CoV‐2 variants correlates with COVID‐19 severity

HLA (2023)

Vishal Rao Ushashi Banerjee Narmada Sambaturu Sneha Chunchanur R. Ambica

Heterogeneity in susceptibility among individuals to COVID‐19 has been evident through the pandemic worldwide. Cytotoxic T lymphocyte (CTL) responses generated against pathogens in certain individuals are known to impose selection pressure on the pathogen, thus driving emergence of new variants. In this study, we probe the role played by host genetic heterogeneity in terms of HLA‐genotypes in determining differential COVID‐19 severity in patients. We use bioinformatic tools for CTL epitope prediction to identify epitopes under immune pressure. Using HLA‐genotype data of COVID‐19 patients from a local cohort, we observe that the recognition of pressured epitopes from the parent strain Wuhan‐Hu‐1 correlates with COVID‐19 severity. We also identify and rank list HLA‐alleles and epitopes that offer protectivity against severe disease in infected individuals. Finally, we shortlist a set of 6 pressured and protective epitopes that represent regions in the viral proteome that are under high immune pressure across SARS‐CoV‐2 variants. Identification of such epitopes, defined by the distribution of HLA‐genotypes among members of a population, could potentially aid in prediction of indigenous variants of SARS‐CoV‐2 and other pathogens.

CTL*

10.1111/tan.15071

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Presumptive diagnosis of brucella epididymoorchitis by modified cold ZN staining of testicular pus sample.

R. D. Kulkarni Sneha Chunchanur G S Ajantha C Shubhada Pavitra Jain

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Mycobacterium species on the cutaneous microbiome of very preterm neonates

Research Square (Research Square) (2021)

Pritik A Shah Varun Govindarajan Ambica Rangaiah Shivashankar Diggikar Sahana Devadas

Abstract The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harbouring on the skin of babies. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead to pathological disease. We conducted this study to understand the neonatal skin microbiome of very preterm neonates admitted to NICU at a tertiary health care setting before and after Kangaroo Mother Care. Next Generation sequencing showed relative abundance for Mycobacterium tuberculosis in 83.33% & 66.67% (p0.285) and Mycobacteroides abscessus in 100% & 93.33%( p0.303) of the very preterm neonates on the skin microbiome before and after KMC respectively. The mere presence of Mycobcaterium species as commensals or as potential pathogens, is alarming due to the risk of early exposure and incidence of tuberculosis right from birth. These findings, in our view, are the first findings to be established in such a setting.

10.21203/rs.3.rs-636873/v1

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