Communicable Disease Management Flashcards
NPHL roles
Indicator-based surveillance
* Detect changes in frequency of serotypes and genotypes of pathogens, in order to raise alert for early intervention
Event-based surveiilance
* clusters e.g. diarrhoea, respiratory, fever
* unusual cases, imported severe cases
Support Vaccine Policy
* Serotype and genotype changes e.g. influenza, pneumococcus
* Seroprevalence of vaccine preventable disease
New Agents
* To develop and evaluate tests : laboratory-developed or commercial
Rare Pathogens and Biothreats
* E.g. Anthrax, Monkeypox, Botulism
Microscopy
- Light microscopy: Gram stain
- Fluorescent microscopy
- Electron Microscopy
Bacteria
- Culture : agar plates, enrichment (broth)
- Identification : biochemicals, MALDI-ToF, sequencing
- Antimicrobial susceptibility : disc, E test, commercial broth microdilution
- Serotyping e.g. pneumococcus, salmonella
- Antigen detection
- Molecular: PCR, sequencing
Viruses
- PCR
- Antigen detection
- Sequencing
- Virus isolation : tissue cell lines
- Virus neutralization tests, PRNT
Parasites
- Microscopy : wet, Trichrome stain, Giemsa, acid-fast, immunofluorescence
- PCR, sequencing
- (culture – rare)
Molecular Methods
Molecular methods
* PCR, others, multiplex
* Sequencing
* Typing
- Older: e.g. MLST, MLVA
- WGS : with good bioinformatics
* Metagenomic approaches
Antibody detection (serology)
- Enzyme immunoassay (EIA, ELISA)
- Immunofluorescent antibody (IFA)
- Haemagglutination inhibition (HAI)
- Chemiluminescent (mostly commercial)
- Virus neutralization, PRNT
Case Study 1
Case Study 1:
* Food poisoning incident : 154 cases at a hawker centre
* Consumption of contaminated “Indian rojak” from a popular hawker stall
Identification of Pathogen
* 16 Isolates of Vibrio parahaemolyticus are identified
* Serotyping further performed
➢ 15 Outbreak isolates have serotype O4: K55
➢ 1 isolate (number 22) have serotype O3:K6
- PCR typing (presence/absence) of thermo stable direct hemolysin (TDH) and TDH-related hemolysin (TRH)
➢All 16 isolates tdh (+), and trh (-) - Film Array (Gastrointestinal Panel): Multiplex PCR allowing detection of common GI pathogens within an hour
- Limitations: Does not identify serotype
1 machine replaces 3 machines : Nucleic acid extraction Polymerase Chain Reaction Detection and Analysis
MALDI-TOF
- MALDI-TOF: Use of Mass Spectrometry to identify pathogen
- Limitations: May not be able to able to differentiate between closely related species
- e.g. Burkholderia pseudomallei vs. B. mallei , E. coli vs Shigella sp., Bacillus anthracis vs. B. cereus, Clostridium sporogenes vs. C. botulinum
- A thin film is spread onto a MALDI target plate.
- Add HCCA matrix.
- Plate is placed in the MALDI equipment.
- Mass spectra generated.
- Bacteria identified by matching mass spectrum with database.
Case 2
Case 2:
* Spike in Typhoid Cases in July 2021
* NPHL received 16 Salmonella Typhi isolates form 14 different cases
➢4 different MLVA types – 29, 35, 36, 37 identified
➢10 isolates were found to have the same MLVA type 35
➢1 Isolate had MLVA type 37 – similar to type 35 with 1 repeat difference
- (Multiplex PCR – optional)
- Bacteria culture on selective media e.g. XLD, DCA
- Serotyping : O, H (Kauffman-White scheme) – obtain “name” e.g.
Salmonella Stanley (Salmonella enterica subspecies enterica serovar Stanley) - Molecular typing e.g. MLVA
- Whole genome sequencing (WGS)
- WGS confirmed same genotype –likely common source
Case 4
- In December 2012, 4 Singaporeans returned from country X with
malaria
➢Different groups who did cycling/ water sports activities - Epi-Link: All slept at least once in the same kelong
- Microscopy to identify presence of parasites, subspecies of malaria and stages of malaria
➢Use of Giemsa staining
➢Thick blood film – for identification of parasites
➢Thin blood film – to assess the morphology of the parasites for species and stages - Nested-PCR for Pf genotyping
– allows Subtyping into families - 4 samples had Pf msp1- K1 subtype
- 4 samples had Pf msp2 – IC/3D7 subtype
- Microsatellite profile generated with 6 highly polymorphic markers
- Identical Microsatellites
Follow-up Actions:
✓ Contacted other members of cycling and jet skiing groups. All reported to be well. Advised to seek medical treatment if became unwell
✓Informed WHO IHR of cluster, and enquired about malaria situation in
Country X
TB case
Index Case’s Unit
- 3 cases
- Index MDR TB case diagnosed in Feb 2012.
- Household members - 2 household members diagnosed with active MDR TB in May 2012 and Oct 2015 respectively.
2nd Unit
- One case diagnosed with MDRTB in Apr 2014
3rd Unit
- One case diagnosed with MDRTB in Oct 2015
4th Unit
- One case diagnosed with MDRTB in May 2016
- WGS can confirm relatedness of the isolates
Index case of Blk X = Index case of gaming centre
- MDR-TB cluster involving 5 patrons in 2012/13
Drug Resistance Prediction
TB WGS Resistance Prediction
- Association of the mutation with phenotypic drug resistance, including frequency of mutation
- Amount of evidence that mutation is associated with DR
- MIC distribution
Drug resistance confidence database -> NPHL confidence score
Influenza cases
community, severe case, outbreak surveillance
- Virus Identification by real time PCR assays
- Influenza type (A or B)
- Influenza A subtypes
- Influenza B lineages - Virus Isolation by cell culture
- Sent to WHO for antigenic characterization - Virus characterization by sequencing
- Identify important mutations
Global Influenza Surveillance and
Response System (GISRS)
National Influenza Centres
* Collect Specimens from ILI cases
* Isolate and Identify viruses
* Send viruses to a WHO CC
* Collect epidemiological information
World Health Organization(Geneva)
* Analyze influenza viruses received
* Provide data for annual vaccine recommendations
* Prepare and distribute candidate vaccine strains <-> vaccine producers
WHO Collaborating Centres
* Collect information for the Weekly Epidemiological Record and WWW for distribution
* Make annual vaccine recommendations
