BIOINFORMATICS

AND BIOSENSORS
DR. MONICA PATHANIA
BIOINFORMATICS
• Bioinformatics is a field of science that combines
biology and computer science to collect, manage,
analyze, and interpret biological data.
• It involves the development and application of
computational techniques and tools to understand
and solve complex biological problems.
Bioinformatics tools role in various
aspects of :

1. Diagnosing infectious diseases

2. Monitoring outbreaks
3. Studying antimicrobial resistance (AMR)
4. Understanding the genetic diversity of pathogens.
Diagnosing Infectious Diseases:
• Pathogen Identification: Tools like Kraken and IDseq
enable rapid and accurate identification of pathogens
from clinical samples, such as blood, tissue, or swabs.
• Kraken: A taxonomic sequence classifier that identifies
and characterizes bacteria & viruses from genomic
data.
• IDseq: A cloud-based platform for pathogen detection
and surveillance using metagenomic sequencing data.
• Genomic Variability: By sequencing the genomes of
pathogens, can identify genetic variations that may
affect the virulence or drug resistance of the
microorganism, aiding in diagnosis and treatment
decisions.
• Molecular Diagnostics: Tools for designing PCR
primers, like Primer3, help create specific assays for
pathogen detection.
Monitoring Outbreaks:
• Epidemiological Analysis: Bioinformatics tools, such as
MLST (Multilocus Sequence Typing )and phylogenetic
tree construction tools, help trace the origin and
transmission of infectious diseases during outbreaks.
• Genomic Epidemiology: Nextstrain and Microreact
allow real-time tracking of pathogen evolution and
spread, aiding in outbreak management and control.
It is primarily used for RNA viruses like influenza, HIV,
and SARS-CoV-2.
Studying Antimicrobial Resistance (AMR):

• AMR Gene Detection: Tools like ResFinder and CARD

identify acquired antibiotic resistance genes in
bacterial genomes.
• Genomic Analysis
ResFinder
• ResFinder is a bioinformatics tool developed by the
Center for Genomic Epidemiology.
• ResFinder compares the genomic sequences of
bacteria against a comprehensive database of known
antibiotic resistance genes.
CARD
• (Comprehensive Antibiotic Resistance Database)
CARD is a comprehensive resource and database of
antibiotic resistance genes, their associated proteins,
and their mutations
• Users can search the database by gene name,
sequence, or protein family. CARD also includes
resistance prediction models and tools for mutation
detection.
Understanding Genetic Diversity of Pathogens:

• Phylogenetic Analysis: Bioinformatics tools for

constructing phylogenetic trees, such as RAxML and
PhyML, allow researchers to assess the relatedness of
pathogen strains.
• Genome Comparison: Tools like Microbial Genomes
Atlas (MiGA) and PATRIC (Pathosystems Resource
Integration Center)enable comparative genomics,
facilitating the study of genetic diversity and evolution
within pathogen populations
• Enterobacteriaceae Family:
• Streptococcus Genus:
• Vibrio Genus Building phylogenetic trees to understand the
evolutionary relationships between different Vibrio strains
and their adaptation to different environments
• Mycobacterium Genus: Analyzing the genetic diversity and
evolution of Mycobacterium species, tuberculosis, the
causative agent of tuberculosis.
• Constructing phylogenetic trees to track the spread of drug-
resistant strains and investigate the population structure.
BIOSENSORS
Biosensors are analytical devices or tools that
combine a biological component (such as enzymes,
antibodies, or cells) with a physicochemical detector to
detect and quantify specific biological molecules or
biochemical reactions.
 USE
• Pathogen Detection: Biosensors can rapidly detect
specific microbial pathogens or biomarkers in clinical
samples, enhancing diagnosis speed and accuracy.
• Monitoring Environmental Microbes: They're used to
monitor microbial pollution in water, soil, or air,
ensuring safety.
• Food Safety: Biosensors detect harmful microbes in
food, preventing outbreaks.
• Bioprocess Control: In biotechnology, they monitor
microbial cultures for optimal growth and product
yield.
• Antibiotic Resistance: Biosensors can detect antibiotic
resistance genes, aiding in surveillance and treatment
decisions.
 Pathogen Detection And
Identification

• Biosensors can be designed to detect specific

microbial pathogens, such as bacteria, viruses, and
fungi, directly from clinical samples (e.g., blood, urine,
or swabs).
• These sensors often employ antibodies or nucleic acid
probes as the biological recognition element to
capture and identify the target pathogen.
How Biosensors Detect Microbial Pathogens:

1. Biological Recognition Element: Biosensors incorporate a

biological recognition element that specifically binds to the
target pathogen. This element can be an antibody,
enzyme, or even a whole cell, depending on the design of
the biosensor.
2. Transducer: The biological recognition event triggers a
change in a physicochemical property, such as electrical
conductivity, optical properties, or mass, depending on the
type of transducer used in the biosensor.
3. Signal Amplification: Some biosensors may include signal
amplification mechanisms to enhance the detection sensitivity.
This could involve enzyme-based amplification or the use of
nanomaterials.
4. Signal Readout: The change in the physicochemical property
is translated into a measurable signal, which can be quantified
and displayed to provide information about the presence and
concentration of the target pathogen.
Antibiotic Susceptibility Testing:

• Biosensors can assess the susceptibility of bacterial

isolates to antibiotics by monitoring their growth and
response in the presence of various antimicrobial
agents.
• Real-time data from biosensors can guide clinicians in
choosing the most effective antibiotic therapy,
helping to combat antimicrobial resistance.
Viral Load Monitoring:

• Biosensors are employed to measure the

concentration of viral particles in clinical samples,
particularly in the context of HIV, hepatitis, and
COVID-19 monitoring.
• Monitoring viral load helps clinicians assess disease
progression and the effectiveness of antiviral
therapy.
Toxin Detection:

• Some biosensors are designed to detect microbial

toxins produced by pathogens, such as toxins
produced by Clostridium difficile or Staphylococcus
aureus.
• Rapid toxin detection assists in the diagnosis of
toxin-mediated diseases and guides treatment
decisions
Microbial Metabolite Analysis:

• Biosensors can measure specific microbial

metabolites or biomarkers associated with
microbial infections, such as urea or glucose levels
in urine.
• Monitoring these metabolites can aid in diagnosing
and managing infectious diseases.
Point-of-Care Testing (POCT):

• Portable biosensors enable on-site and rapid

testing, which is especially valuable in remote or
resource-limited settings.
• POCT biosensors facilitate quick diagnosis and
treatment initiation, reducing the time to results
• Epidemiological Surveillance:

Biosensors are used in the real-time monitoring of

microbial strains during outbreaks, helping to trace
the source and spread of infections.
 Bioinformatics Tools That Are
Commonly Used In Clinical
Microbiology
• Pathogen Identification :
• Kraken
• IDseq
• Antibiotic Resistance Prediction:
• ResFinder
• CARD
• Epidemiological Analysis:
• MLST
• Phylogenetic Tree Construction: RAxML and PhyML
• Viral Load and Subtyping:
• HIV Drug Resistance Database (Stanford HIVdb):
Used for HIV subtyping and drug resistance analysis.
• Influenza Research Database: Provides tools for
influenza virus surveillance, analysis, and subtyping.
• Genomic Epidemiology:
• Nextstrain
• Microreact
• Molecular Diagnostic Tools:
• Primer3
• Microbial Genomic Data Analysis:
• Microbial Genomes Atlas (MiGA)
• PATRIC (Pathosystems Resource Integration Center)
• Clinical Variant Analysis:
• VarSeq: A platform for clinical interpretation of
genetic variants
• Pharmacogenomics Analysis:
• PharmGKB: A resource for pharmacogenomic data
and drug-gene interactions.
• Visualization and Data Integration:
• IGV (Integrative Genomics Viewer): Allows
visualization of genomic data, including variant
calling.
These tools assist clinical microbiologists and
healthcare professionals in diagnosing infectious
diseases, monitoring outbreaks, studying antimicrobial
resistance, and understanding the genetic diversity of
pathogens.
THANK YOU