Detection and classification of Bacteria using Raman Spectroscopy Combined with Multivariate Analysis

S. Sil; R. Mukherjee; N. S. Kumar; Aravind S.; J. Kingston; U. K. Singh

doi:10.14429/dlsj.2.12275

S. Sil Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India
R. Mukherjee Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru-560 012, India
N. S. Kumar Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India
Aravind S. Defence Food Research Laboratory, Mysuru, India-570 011
J. Kingston Defence Food Research Laboratory, Mysuru, India-570 011
U. K. Singh Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India

DOI: https://doi.org/10.14429/dlsj.2.12275

Keywords: Raman Microspectroscopy, Pathogen, Multivarate Analysis, Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), PC-LDA

Abstract

Vibrational spectroscopic techniques have advantages over conventional microbiological approaches towards identification & detection of pathogens. Since unique spectral fingerprint is obtained, one can identify very closely related bacteria using such methods. In this study Raman microspectroscopy in combination with chemometric method has been used to classify four strains of E. coli (two pathogenic & two non-pathogenic). Different multivariate approaches such as hierarchical cluster analysis, principal component analysis & linear discriminant analysis were explored to obtain efficient classification of the Raman signals obtained from the four strains of E.coli. It was observed that multivariate analysis was able to classify the bacteria at strain level. Linear discrimination analysis using PC scores (PC-LDA) was found to give very good result with as high as 100% accuracy. This hybrid technique (Raman spectroscopy & multivariate analysis) has tremendous potential to be developed as a tool for bacterial identification.

Author Biographies

S. Sil, Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India

Dr Sanchita Sil obtained his PhD from the Indian Institute of Science,
Bengaluru, in 2015. Currently working in Defence Bioengineering
& Electromedical Laboratory (DEBEL), Bengaluru. Her areas of
research spans over understanding molecular structure of materials
using Raman spectroscopic techniques like SERS and development of
novel Raman based methods for materials and biological applications.
She is also interested in the area of development of carbon based
materials for environmental applications.

R. Mukherjee, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru-560 012, India

Ms Ria Mukherjee is a PhD student (CSIR-SRF) under the guidance
of Prof. S. Umapathy, IPC department, IISc. She has obtained her
MSc (Chemistry) from IIT Guwahati. Currently, she is working on
Raman spectroscopy and its biological applications. Her area of
interest is biophotonics and biophysical research

N. S. Kumar, Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India

Dr N.S. Kumar received his PhD from Sree Chitra Tirunal Institute
of Medical Science and Technology, Thiruvananthapuram. He
joined DRDO in 1991 as Scientist ‘B’ and is currently the Joint
Director at Defence Bioengineering & Electromedical Laboratory,
Bengaluru. His areas of interest are design and development of Naval
materials, biomedical devices, NBC protective equipment and air
quality management. His current interest spans over CBRN defence,
biomaterials and air quality mangement.

Aravind S., Defence Food Research Laboratory, Mysuru, India-570 011

Mr Aravind S. is a PhD student (DRDO-SRF) in Microbiology
Division, DFRL, Mysuru. He obtained his MSc in Biotechnology from
VIT University. His areas of interest includes developing detection
methods that differentiate live and dead food borne pathogens and
developing mucosal vaccines for protection against E. coli O157:H7.

J. Kingston, Defence Food Research Laboratory, Mysuru, India-570 011

Dr J.J. Kingston obtained his PhD in Microbiology from Indian
Agricultural Research Institute, New Delhi. He subsequently
completed his post-doctoral research from Department of Biological
Sciences, University of Delaware, Newark, DE with DST-BOYSCAST
fellowship. Currently working in Defence Food Research Laboratory,
Mysuru. His broad areas of interest are diagnostic microbiology,
molecular markers, and structural vaccinology. He is interested in
developing diagnostic assays for the detection of food borne pathogens
and toxins, markers for application in molecular epidemiology and
generating isogenic mutants for use as live attenuated vaccines.

U. K. Singh, Defence Bioengineering & Electromedical Laboratory, Bengaluru-560 093, India

Dr U.K. Singh completed his MSc and MTech in Computer Science
from DAVV, Indore and obtained his PhD in Soft Computing from
University of Hyderabad. Currently working as Director, Defence
Bioengineering and Electromedical Laboratory, Bengaluru. Prior
to this assignment, he was Project Director (Weapon Systems) for
Ballistic Missile Programme at Hyderabad. He is a recipient of
DRDO Award for Path-breaking Research/Outstanding Technology
development and Laboratory Scientist of the Year Award (Lab level-
DRDO Award).