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  1. Article ; Online: Phylogenetic diversity of

    Chunchanur, Sneha K / Venugopal, Shwetha J / Ambica, R / Dakshayani, B

    Indian journal of medical microbiology

    2020  Volume 37, Issue 3, Page(s) 438–441

    Abstract: Scrub typhus has re-emerged as an important cause of acute febrile illness in India. There is a dearth of information on strain diversity of Orientia tsutsugamushi from Karnataka, India, hence the present study sought to address this issue. One hundred ... ...

    Abstract Scrub typhus has re-emerged as an important cause of acute febrile illness in India. There is a dearth of information on strain diversity of Orientia tsutsugamushi from Karnataka, India, hence the present study sought to address this issue. One hundred clinically suspected cases of scrub typhus/rickettsiosis (as per the DHR-ICMR guidelines) were included. Nested-polymerase chain reaction (PCR) for 56-kDa gene and phylogenetic analysis was performed. PCR was positive in 22 cases and phylogenetic analysis showed the presence of different strains, with predominance of clustering (57%) with Gilliam-type for the first time in Karnataka. Knowledge of genetic diversity has implications in development of diagnostics and vaccine.
    MeSH term(s) DNA, Bacterial/genetics ; Genotype ; Humans ; India ; Orientia tsutsugamushi/classification ; Orientia tsutsugamushi/genetics ; Phylogeny ; Polymerase Chain Reaction ; Scrub Typhus/classification ; Scrub Typhus/genetics ; Sequence Analysis, DNA
    Chemical Substances DNA, Bacterial
    Language English
    Publishing date 2020-08-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1038798-5
    ISSN 1998-3646 ; 0255-0857
    ISSN (online) 1998-3646
    ISSN 0255-0857
    DOI 10.4103/ijmm.IJMM_19_267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2639: Show issues Location:
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  2. Article ; Online: Culture-Independent Raman Spectroscopic Identification of Bacterial Pathogens from Clinical Samples Using Deep Transfer Learning.

    Singh, Saumya / Kumbhar, Dipak / Reghu, Dhanya / Venugopal, Shwetha J / Rekha, P T / Mohandas, Silpa / Rao, Shruti / Rangaiah, Ambica / Chunchanur, Sneha K / Saini, Deepak Kumar / Umapathy, Siva

    Analytical chemistry

    2022  Volume 94, Issue 42, Page(s) 14745–14754

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Spectrum Analysis, Raman/methods ; Bacteria ; Machine Learning ; Nucleic Acids ; Plant Extracts
    Chemical Substances Nucleic Acids ; Plant Extracts
    Language English
    Publishing date 2022-10-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c03391
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4033: Show issues Location:
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  3. Article ; Online: Virulence gene mutations as a differentiator of clinical phenotypes: insights from community-acquired uropathogenic

    Yadav, Manisha / Pundir, Swati / Kumari, Rajesh / Kumar, Arvind / Venugopal, Shwetha J / Panigrahy, Rajashree / Tak, Vibhor / Chunchanur, Sneha K / Gautam, Hitender / Kapil, Arti / Das, Bimal / Sood, Seema / Salve, Harshal Ramesh / Malhotra, Sumit / Kant, Shashi / Hari, Pankaj / Chaudhuri, Susmita / Mohapatra, Sarita

    Microbiology (Reading, England)

    2022  Volume 168, Issue 4

    Abstract: ... ...

    Abstract Uropathogenic
    MeSH term(s) Escherichia coli Infections ; Escherichia coli Proteins/genetics ; Female ; Humans ; Mutation ; Phenotype ; Pregnancy ; Urinary Tract Infections ; Uropathogenic Escherichia coli/genetics ; Virulence/genetics ; Virulence Factors/genetics
    Chemical Substances Escherichia coli Proteins ; Virulence Factors
    Language English
    Publishing date 2022-05-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.001161
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Antibiotic resistance of uropathogens among the community-dwelling pregnant and nonpregnant female: a step towards antibiotic stewardship.

    Mohapatra, Sarita / Venugopal, Shwetha J / Kalaivani, Mani / Kant, Shashi / Tak, Vibhor / Panigrahy, Rajashree / Chunchanur, Sneha K / Kocher, Deepak / Behera, Birasen / Pundir, Swati / Chaudhuri, Susmita / Gautam, Hitender / Sood, Seema / Das, Bimal Kumar / Kapil, Arti / Kumar, Arvind / Kumari, Rajesh / Ambica, R / Hari, Pankaj /
    Malhotra, Sumit / Salve, Harsal Ramesh

    BMC infectious diseases

    2022  Volume 22, Issue 1, Page(s) 939

    Abstract: Background: Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized ... ...

    Abstract Background: Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized that the uropathogens isolated from pregnant women would be more susceptible to antibiotics compared to those isolated from nonpregnant women, thus will be helpful in formulating separate empiric guideline for pregnant women based on the resistance pattern.
    Methods: This was a prospective cross-sectional study conducted over a period of 2 years in which females with the clinical diagnosis of either cystitis or asymptomatic bacteriuria during pregnancy were included from the community settings. Uropathogen species and their antimicrobial resistance pattern were compared between the pregnant and nonpregnant groups. After accounting for centre-to-centre variation and adjusting for age and socio-economic status, the adjusted odds ratio for antibiotic resistance was calculated and compared between pregnant and nonpregnant women using logistic regression analysis.
    Results: A total of 1758 women (pregnant: 43.3%; nonpregnant: 56.6%) were screened in the study over a period of 2 years, out of which 9.3% (163/1758) were having significant bacteriuria. Escherichia coli and Klebsiella pneumoniae were the two commonest uropathogen in both the groups; their prevalence being 83.6% in pregnant women and 85.2% in nonpregnant women, respectively. Resistance against ampicillin, cefixime, cefoxitin, ceftazidime, ceftriaxone and amoxicillin-clavulanic acid were found significantly lower in the pregnant women compared to nonpregnant. After adjusting the age and socio-economic status accounting for centre-to-centre variation, the odds of resistance for cefixime, amoxicillin-clavulanic acid and co-trimoxazole were found lower and statistically significant among the pregnant women group.
    Conclusions: The antimicrobial resistance was significantly higher among the community-dwelling nonpregnant women compared to pregnant women in case of few antibiotics. The study highlighted the need of building local antibiogram that could help to initiate the empirical treatment and thus prevent emergence of antimicrobial resistance.
    MeSH term(s) Female ; Humans ; Pregnancy ; Bacteriuria/diagnosis ; Amoxicillin-Potassium Clavulanate Combination/therapeutic use ; Antimicrobial Stewardship ; Cefixime/therapeutic use ; Urinary Tract Infections/drug therapy ; Urinary Tract Infections/epidemiology ; Cross-Sectional Studies ; Prospective Studies ; Independent Living ; Drug Resistance, Microbial ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Escherichia coli
    Chemical Substances Amoxicillin-Potassium Clavulanate Combination (74469-00-4) ; Cefixime (97I1C92E55) ; Anti-Bacterial Agents
    Language English
    Publishing date 2022-12-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-022-07914-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Diagnostic potential of 16 kDa (HspX, α-crystalline) antigen for serodiagnosis of tuberculosis.

    Kaushik, Amit / Singh, Urvashi B / Porwal, Chhavi / Venugopal, Shwetha J / Mohan, Anant / Krishnan, Anand / Goyal, Vinay / Banavaliker, Jayant N

    The Indian journal of medical research

    2012  Volume 135, Issue 5, Page(s) 771–777

    Abstract: Background & objectives: Tuberculosis (TB) is a public health problem worldwide. Rapid and accurate diagnosis of tuberculosis is crucial to facilitate early treatment of infectious cases and to reduce its spread. The present study was aimed to ... ...

    Abstract Background & objectives: Tuberculosis (TB) is a public health problem worldwide. Rapid and accurate diagnosis of tuberculosis is crucial to facilitate early treatment of infectious cases and to reduce its spread. The present study was aimed to evaluation of 16 kDa antigen as a serodiagnostic tool in pulmonary and extra-pulmonary tuberculosis patients in an effort to improve diagnostic algorithm for tuberculosis.
    Methods: In this study, 200 serum samples were collected from smear positive and culture confirmed pulmonary tuberculosis patients, 30 tubercular pleural effusions and 21 tubercular meningitis (TBM) patients. Serum samples from 36 healthy, age matched controls (hospital staff), along with 60 patients with non-tubercular respiratory diseases were also collected and evaluated. Humoral response (both IgG and IgA) was looked for 16 kDa antigen using indirect ELISA.
    Results: Sensitivity of detection in various categories of pulmonary TB patients ranged between 73.8 and 81.2 per cent. While in the extra-pulmonary TB samples the sensitivity was 42.8 per cent (TBM) and 63.3 per cent (tubercular pleural effusion). The test specificity in both the groups was high (94.7%). All of the non-disease controls were negative. Among non-tubercular disease controls, five patients gave a positive humoral response against 16 kDa.
    Interpretation & conclusions: Serodiagnostic tests for TB have always had drawbacks of suboptimal sensitivity and specificity. The antigen used in this study gave encouraging results in pulmonary TB only, while in extra-pulmonary TB (tubercular meningitis and tubercular pleural effusion), this has shown a limited role in terms of sensitivity. Further work is required to validate its role in serodiagnosis of TB especially extra-pulmonary TB.
    MeSH term(s) Adult ; Antigens/blood ; Antigens, Bacterial/blood ; Bacterial Proteins/blood ; Female ; Humans ; Immunity, Humoral ; Immunoglobulin A/blood ; Immunoglobulin A/immunology ; Immunoglobulin G/blood ; Immunoglobulin G/immunology ; Male ; Middle Aged ; Mycobacterium tuberculosis/immunology ; Pleural Effusion/blood ; Pleural Effusion/diagnosis ; Sensitivity and Specificity ; Serologic Tests ; Tuberculosis, Meningeal/blood ; Tuberculosis, Meningeal/diagnosis ; Tuberculosis, Pulmonary/blood ; Tuberculosis, Pulmonary/diagnosis
    Chemical Substances Antigens ; Antigens, Bacterial ; Bacterial Proteins ; HspX protein, Mycobacterium tuberculosis ; Immunoglobulin A ; Immunoglobulin G
    Language English
    Publishing date 2012-07-06
    Publishing country India
    Document type Journal Article
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    Database MEDical Literature Analysis and Retrieval System OnLINE

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