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Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy

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Abstract

Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria.

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Acknowledgments

S. Kumar acknowledges DST for INSPIRE fellowship. S. Umapathy acknowledges the Department of Science and Technology (DST Grant No. SR/S2/JCB-52/2009) and the Department of Biotechnology (Grant No. BT/01/CEIB/09/IV/05), Government of India, for financial support. S. Umapathy is a J. C. Bose Fellow of the Department of Science and Technology. D.K. Saini acknowledges the Department of Biotechnology (DBT Grant No. BT/PR3260/BRB/10/967/ 2011; BT/PR17357/MED/29/1019/ 2016), Government of India; DST-FIST [SR/FST/LS11-036/2014(C)], UGC-SAP [F.4.13/2018/DRS-III (SAP-II)], and DBT-IISc Partnership Program Phase-II (BT/PR27952-INF/22/212/2018) for infrastructure and financial support and Infosys Foundation for financial support.

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Authors and Affiliations

  1. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India

    Srividya Kumar, Goutam Kumar Chandra & Siva Umapathy

  2. Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India

    Renu Gopinathan & Deepak Kumar Saini

  3. Department of Physics, NIT Calicut, Calicut, Kerala, 673601, India

    Goutam Kumar Chandra

  4. Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India

    Siva Umapathy

  5. Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India

    Deepak Kumar Saini

  6. Centre for Infectious Diseases Research, Indian Institute of Science, Bangalore, 560012, India

    Deepak Kumar Saini

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  1. Srividya Kumar
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Kumar, S., Gopinathan, R., Chandra, G.K. et al. Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy. Anal Bioanal Chem 412, 2505–2516 (2020). https://doi.org/10.1007/s00216-020-02474-2

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