This presentation provides an overview of microbial genomics with focus on its application for surveillance of pathogens & drug resistance and drug discovery.

1. Microbial Genomics and Surveillance: An
Overview Snapshot for a Layman’s
Understanding
Dr. Iwalokun, BA
Molecular Biology & Biotechnology Dept
NIMR, Lagos

2. Presentation Overview
• Microbial Genomics:
– Definition , Necessity and Goals
• Surveillance
– Definition, Essence and for what?
• Microbial Genomics and Surveillance
– Dynamics, Pattern of Interactions and drug resistance
Perspectives
• Nigerian Situation, Regarding Genomics
• & Way Forward
• Conclusion
• Acknowledgment

3. Microbial Genomics: Definitions
• Microbial Genomics can be defined as a component of Microbial
Genetics, which deals with:
– Sequencing
– Mapping &
– Functional analysis
Of genes and their genetic variants in the genomes of
microorganisms.
• Sequencing entails knowing the order of arrangement of bases
that constitute the genome (whole genetic content) of a
microorganism.
• Mapping means knowing the order of arrangement of genes in
the genome of microorganism under study.
• Functional analysis is the method of knowing the functions of the
Identified genes and their determinants (environment, genetic and
epigenetic) .

5. Genomics: A Universal Language
Not Phenotype, But Excellent for
Phenotype Prediction

6. Microbial Genomics: Why?
• For a better understanding of the biology, epidemiology, evolution
and interactions of microorganisms with the environment, animals
and humans.
• To understand the mechanism of emergence, re-emergence and
spread of pathogens of global health importance
• To infuse Information Technology into Life Science.
• To enhance the use of Computational Biology & Bioinformatics to
understand microbial life: physiology, pathogenesis, ecology,
adaptation, evolution etc better
• To drive One Health.
• To drive the development of new diagnostics.
• To improve taxonomy of microorganisms.
……

7. Virology
Medical Microbiology
Environmental
Microbiology
Mycology
Parasitology
Areas of Microbial Genomics.

8. C
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FUNCTIONAL GENOMICS
Branches of Genomics.

9. Components of Bioinformatics.
Bioinformatics: A key player in Pathogen genomics

10. Bioinformatics and Application areas for Pathogen Genomics.

11. Databases for Pathogen Genomics: Repositories of
Computation Tools & Metadata

12. The Basis of Genome Evolution.

13. Microbial Genomics: Why?
.
• To comprehend the global problem of antibiotic resistance
• To improve surveillance, early detection of infectious
disease outbreaks, outbreak investigation and other
outbreak ending responses.
• To enable the development new treatment interventions
• To accelerate drug discovery……
• To drive new idea, workflow and data integration in the
conduct of Surveillance and Epidemiological studies

14. Genomics Goals.

15. STOP

16. Genomics at a glance.
The
Big Data
Output
Outcome

17. Surveillance
• Systematic way of monitoring pathogens for properties
associated with health risks or diseases.
– Carriage/Presence (Human, Animal, Environmental)
– Emergence
– Transmission
– Evolution
– Pathogenesis
– Drug Resistance
– Phage gene acquisition
– Horizontal Gene Transfer
– Tracking epidemics
– etc
• To be able to provide actionable public health actions
(E.g. infection control measures; drug discovery &
development, drug trial, vaccine development, vaccine
trial, Epidemiology, Mass Drug Administration, Targeted
Vaccination, Mass Vaccination Campaign etc)

19. Current Direction of Routine Surveillance.

20. Microbial Genomics for Surveillance
• Knowing the genomes of pathogens of interest
– Genome Project
• Sequencing, gene prediction, gene content &
organization.
• Gene SNP identification & Phylogeny Construction for
strains (locally, temporally & geographically/spartially)
• Metagenomics (No culture!!)
• Knowing the databases/Workflow./Data Analysis Plan
– Genome Applications
• Epidemiology
• Functional Genomics
• Comparative Genomics
• Structural Genomics
• Diagnostics
• Drug prediction, design and development
• Vaccine discovery & development

25. Know the database

26. Know the database

27. Know the database

28. Know the database

29. Growth of Neisseria meningitidis Genome Library in
England & Wales (2010 -2015)

31. Growth of Genomics & Functional Genomics

43. Quality Checkpoints from Sample Prep through
Sequencing to Bioinformatics

48. Velvet: A read assembly tool

51. Mauve for contigs ordering and multiple genome comparison

52. Artemis and ACT : for genome viewing and mapping to
reference genomes.

53. BRIG (BLAST Ring Image Generator) for multiple genome comparison

55. NCBI Platform for submission of
pathogen genome sequences:
environmental, food/animal,
humans (One Health)

56. Data Analysis Plan: An Essential component of Pathogen Genomics

61. Antibiotics: the mainstay of Prevention, Treatment &
Cure in Medicine

62. Antibiotic use by countries.

73. Antibiotic Resistance Timeline.

82. BRICS
MINT

90. Global trade and travels are drivers of superbug
transmission across the globe.

93. Four Key strategies of reducing the burden
of Antibiotic Resistance.

94. Anti-TB Drugs Development Pipeline

99. Nigerian Situation regarding
Genomics
• Preparatory Phase
– Laboratory strengthening for
• Surveillance
• Pathogen detection
• Resistance gene detection (e.g ESBL genes)
– Collaboration
• Research institute vs University
• North-south
• Multidisciplinary (One Health Approach)
– Build Bioinformatics Capacity
• Algorithms + Databases (Learning to use and building)
– Develop a robust Surveillance System
– Publish in peer reviewed journals
– Grant writing capacity

100. Conclusion
• Pathogens Genomics offers of new way of getting actionable
public health information from pathogens beyond the reach of
culture and identification, other phenotypic tests and few gene
based molecular typing methods.
• The currency of genomics are the reads derived from whole
genome sequencing and assembled for genome annotation and
functional genomics
• Genomics is now the best tool for pathogen surveillance and
Outbreak response.
• The level of research in microbial genomics in Nigeria is at the
preparatory phase
• Way forward include STEM education integration into Biology
education, laboratory strengthening and human capacity
building for grantmanship, high level scientific publication,
surveillance, rapid outbreak detection and effective outbreak
response, drug discovery and vaccine discovery,

101. • THANK YOU ALL!!