Pathogen Genomes Flashcards
Why sequence pathogen genomes
- Provides the highest resolution information about pathogen genome sequence
- Relatively small genome- easier and faster to sequence
- Facilitates discovery of novel genomic variation at scale
- Facilitates understanding of pathogen biology and epidemiology
- Support outbreak management
- Informs research efforts
How is Sequencing pathogen genomes important in disease surveillance and outbreak response
- Early detection: By analysing the genetic sequence of pathogens, scientists can detect new or emerging strains quickly, allowing for a faster response to outbreak
- Tracking transmission: Genomic data helps trace the spread of infections, identifying how and where disease are spreading, which is vital for controlling outbreaks
How is Sequencing pathogen genomes important in understanding pathogen evolution
- Mutation monitoring: Pathogen can mutate over time. Genomics helps track these changes, which can affect how infectious or deadly a pathogen becomes.
- Antibiotic resilience: It can identify genetic markers associated with resistance to antibiotics or antiviral drugs, guiding treatment strategies
How is Sequencing pathogen genomes important in vaccine and therapeutic development
- Target identification: Understanding the genetic makeup of pathogens helps in identifying targets for vaccines and treatment
- Vaccine effectiveness: Genomic can monitor ho well vaccines are working and if pathogen are evolving to escape vaccine- induced immunity
How is Sequencing pathogen genomes important in Personalised medicine and public health
- Tailored treatment: Genomic information can be used to develop personalised treatment plans based on the specific stain of pathogen infecting a patient
- Informed decisions: Data from pathogen genomic s can inform public health policies and strategies, ensuring they are based on the most current and accurate information
In pathogen sequencing what are the considerations for which technology to use (9)
- Type of sequencing information required - pathogen identification versus surveilllance of pathogen evolution
- Type of pathogen and what we know about it
- Type of sample
- Require turn around times
- Where and how sequencing is being deployed
- Size, weight and power requirements and how easy it is to move the tech
- Cost related to equipment
- Availability of reagents and consumable with associated procurement pipelines including transport and appropriate storage
- Established personnel and support for trouble shooting, protocols and pipelines for analysis
Characterise metagenomics vs targeted sequencing
Metagenomics- genomic material in a sample which typically contains a mixed microbial community , is extracted directly from the sample and sequenced using unbiased, non targeted and sequence - independent methods
Targeted- conserved regions of the genome shared by an entire group of microbes are targeted (So specific gene)
Challenges with databases for pathogens
Databases for pathogens - fragmented and poor curation.
Many overlap in term of their coverage and vary in terms of the type and scope of information that they contain.
Key consideration of sequencing and data analysis of pathogen
- Sequencing considerations- sample handling and preparation, resources needed.
- Computing and bioinformatics— availability of computing engineering expertise, infrastructure and bioinformatics expertise. Training needs
Data sharing- increase equitable access to pathogen genome data
Explain uses of genome sequencing for surveillance
- Identifying disease origins
- Transmission dynamics: tracking person to person or how transmission is occurring
- Monitor viral evolution within or between people
- Tracking disease prevalence : frequency of infection
- Outbreak investigation
Explain uses of genome sequencing for diagnosis and infection control
- Pathogen diagnosis
- Detection of mixed infection/ co-infection
- Outbreak management; the use of sequencing can support conventional infection control efforts to determine the source
4, sequencing can be used to understand the genetic mechanisms underlying drug resistance or susceptibility - Determine vaccine suitability
Explain uses of genome sequencing for research diagnosis
- Development of novel therapeutics and vaccines
- Informing diagnostic tests
- Characterisation of virulence factors and resistance markers
- Improving understanding of virus biology : viral mutation rates and rare variant detection
- Understanding the link with disease severity and susceptibility ; stratify patients for prevention or treatment measures
