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Laboratory Testing Services

This section outlines investigations offered by all the departments of the laboratory. These guidelines are applicable for routine specimen referrals.

Please note - Potential outbreaks are managed on a case by case basis following contact with the Laboratory and Epidemiology divisions for further guidance.

Matrix of Disease/Aetiology Specimen Type/s Diagnostic Method and Turnaround Times
*For instructions on specimen collection and transport conditions, please refer to Annex 2

Disease/Aetiologic Agent Method Specimen Turnaround Time (Days) Comment
Bordetella pertussis PCR Nasopharyngeal or throat swab (collected 0 – 3 weeks from onset of cough) 7 Performed at CARPHA for countries without testing capability
Chikungunya PCR* Acute serum (collected 1-5 days from onset of symptoms) 7 Performed at CARPHA for outbreaks
IgM ELISA Convalescent serum (collected 6 - 21 days from onset of symptoms) 14
Cholera Serotyping and Identification
  • Isolate in maintenance media
  • Stool in Cary Blair media
7 Performed at CARPHA for countries without testing capability
Dengue Fever PCR* Acute serum (collected 1 - 4 days from onset of symptoms) 7 Performed at CARPHA for countries without testing capability
IgM ELISA Convalescent serum (collected 5 - 15 days from onset of symptoms) 14
Influenza and other respiratory viruses -
Parainfluenza 1 - 3,
Metapneumovirus,
Adenovirus,
Rhinovirus,
Middle East Respiratory Syndrome Coronavirus (MERS-CoV),
Respiratory Syncytial Virus,
Enterovirus-D68
PCR**
  • Isolate in maintenance media
  • Stool in Cary Blair media
7 Performed at CARPHA for countries without testing capability
Leptospirosis IgM ELISA
PCR (Being implemented)
Serum (collected > 5 days from onset of symptoms) 14 Performed at CARPHA for countries without testing capability
Malaria PCR Blood 7 Performed at CARPHA for countries without testing capability
Contact CARPHA for discussion before submitting
Mayaro virus PCR Serum (collected < 7 days from onset of symptoms) 7 Performed at CARPHA for countries without testing capability
Contact CARPHA for discussion before submitting
Measles virus ELISA IgM Serum - Acute sample (collected < 7 days after onset of rash) 4 Performed under EPI programme
Please check with the EPI manager in-country to ensure appropriate recording of samples prior to submission to CARPHA
ELISA IgG Serum - Convalescent sample (collected 10 to 21 days after collection of acute sample)
PCR
  • NPS (collected < 7 days after onset of rash)
  • Urine (collected < 15 days after onset of rash)
  • NOTE: Urine must be paired with NPS
Meningitis infection (due to Neisseria meningitidis) Antimicrobial Resistance (AMR) testing; Isolate in BHI with glycerol or on Chocolate agar 7-14
  • Performed at CARPHA for countries without testing capability
  • Isolates to be submitted to CARPHA for further characterization.
Meningitis/Sepsis (due to Streptococcus pneumoniae or Haemophilus influenzae) Serotyping (Meningococcus only)
Mumps virus PCR
Virus Isolation
Oral swab (collected 5 days from onset of symptoms) 7
14
Please check with the EPI manager in-country to ensure appropriate recording of samples prior to submission to CARPHA
Norovirus PCR Stool 7 Performed at CARPHA for countries without testing capability
Plague - Yersinia pestis
  • Culture
  • Antimicrobial Resistance (AMR) testing;
  • Blood
  • Biopsy material from bubo
14 CARPHA: to be contacted for discussion if necessary
Sent to CARPHA's Reference Laboratory
Polio Virus PCR
Virus Isolation
Stool (No preservative)
CSF
7
14-21
Performed under EPI programme
Please check with the EPI manager in-country to ensure appropriate recording of samples prior to submission to CARPHA
Non-polio enteroviruses (NPEV) PCR Serum, stool, NPS, Eye swabs, oral fluids (Collect specimens <7days days from onset of symptoms) 7 Performed at CARPHA for countries without testing capability
Rabies (in humans)       Contact CARPHA for discussion before submitting (Sent to CARPHA's Reference Laboratory)
Rotavirus Ag ELISA Stool 7 Performed for countries without testing capability in outbreak situations.
Please contact CARPHA for discussion
Rubella virus ELISA IgM Serum - Acute sample (collected < 7 days after onset of rash) 4 Performed under EPI programme
Please check with the EPI manager in-country to ensure appropriate recording of samples prior to submission to CARPHA
ELISA IgG Serum - Convalescent sample (collected 10 to 21 days after collection of acute sample)
PCR (Being implemented)
  • NPS (collected < 7 days after onset of rash)
  • Urine (collected < 15 days after onset of rash)
  • NOTE: Urine must be paired with NPS
Salmonellosis Serotyping Isolate in Maintenance media 7 - 14 Performed at CARPHA for countries without testing capability
Isolates to be submitted for further characterization
Shigellosis Serotyping Isolate in Maintenance media 14 Performed at CARPHA for countries without testing capability
Isolates to be submitted for further characterization
Toxoplasmosis ELISA IgG
ELISA IgM
Serum, (collected 7 days after onset of symptoms) 14 Performed at CARPHA for countries without testing capability
Tuberculosis (Pulmonary & Extra-pulmonary)
  • Identification (PCR)
  • Drug Sensitivity Testing (PCR)
Sputum, Extrapulmonary samples 4 Performed at CARPHA for countries without testing capability
Selected specimens sent to CARPHA's Reference Laboratory
Typhoid and paratyphoid fever
  • Identification
  • Serotyping
Isolate in maintenance media 7 Performed at CARPHA for countries without testing capability
West Nile Virus PCR CSF/Serum, (collected 7 days after onset of symptoms) 7 Performed at CARPHA for countries without testing capability
Contact CARPHA for discussion before submitting
Yellow fever PCR Single serum 7 Performed at CARPHA for countries without testing capability
Contact CARPHA for discussion before submitting
Zika PCR*
IgM ELISA
  • Serum
  • CSF, Urine, Amniotic fluid NOTE: All of these must be paired with serum sample
7
14
Performed at CARPHA for countries without testing capability.
Zika IgM not done during Dengue outbreaks.
* Samples submitted for Chikungunya, Dengue or Zika that will be tested by PCR are run on a Trioplex panel so there will be results for all three agents
**     Samples submitted for respiratory syndromes are analysed using an algorithm in which they are first tested for Influenza
Specialized Test Panels

Performed on The BioFire® FilmArray® system

CARPHA must be contacted before submitting samples to be tested by this method

MENINGITIS ENCEPHALITIS PANEL
Sample: 0.2 mL of CSF
RESPIRATORY PANEL
Sample: 0.3 mL of nasopharyngeal swab stored in transport medium
GASTROINTESTINAL PANEL
Sample: 0.2 mL stool in Cary Blair transport medium
BACTERIA
  • Escherichia coli K1
  • Haemophilus influenzae
  • Listeria monocytogenes
  • Neisseria meningitidis
  • Streptococcus agalactiae
  • Streptococcus pneumoniae
  • Bordetella pertussis
  • Bordetella parapertussis
  • Chlamydophila pneumoniae
  • Mycoplasma pneumoniae
  • Campylobacter (jejuni, coli, and upsaliensis)
  • Clostridium difficile (toxin A/B)
  • Plesiomonas shigelloides
  • Salmonella
  • Yersinia enterocolitica
  • Vibrio (parahaemolyticus, vulnificus, and cholerae)
DIARRHEAGENIC
E. coli / Shigella
  • Enteroaggregative E. coli (EAEC)
  • Enteropathogenic E. coli (EPEC)
  • Enterotoxigenic E. coli (ETEC) lt/st
  • Shiga-like toxin-producing E.coli (STEC) stx1/stx2
  • E. coli O157
  • Shigella/Enteroinvasive E. coli (EIEC)
VIRUSES
  • Cytomegalovirus (CMV)
  • Enterovirus (EV)
  • Herpes simplex virus 1 (HSV-1)
  • Herpes simplex virus 2 (HSV-2)
  • Human herpesvirus 6 (HHV-6)
  • Human parechovirus (HPeV)
  • Varicella zoster virus (VZV)
  • Adenovirus
  • Coronavirus 229E
  • Coronavirus HKU1
  • Coronavirus OC43
  • Coronavirus NL63
  • Human Metapneumovirus
  • Human Rhinovirus/Enterovirus
  • Influenza A
  • Middle East Respiratory Syncial CoronaVirus (Mers-CoV)
  • Influenza A/H1
  • Influenza A/H1-2009
  • Influenza A/H3
  • Influenza B
  • Parainfluenza (1 – 4)
  • RSV
  • Adenovirus F40/41
  • Astrovirus
  • Norovirus GI/GII
  • Rotavirus A
  • Sapovirus (I, II, IV, and V)
YEASTS
  • Cryptococcus neoformans/gattii
   
PARASITES
   
  • Cryptosporidium
  • Cyclospora cayetanensis
  • Entamoeba histolytica
  • Giardia lamblia
Entomology Specimen Referrals

The following table lists information relevant to the collection and testing of specimens for Entomology investigations.

Note: All specimens sent to the Entomological unit must be accompanied by the following information:

  • Method of specimen collection
  • Date and time of specimen collection
  • Name of specimen collector
  • Country and location
  • Type of habitat (from which collection was made)
Test Specimen Recommended Notes Turnaround Time (Calendar Days)
Insecticide resistance Aedes aegypti mosquito eggs On removal from ovitraps, the paper containing eggs should be placed in a container lined with damp paper towels.
After 2-3 days, the paper should be removed from the container and left to air-dry for 1-2 days. Fold paper in two with the side containing the eggs on the inside.
42
Mosquito identification (larval specimen) Specimen collected and killed in hot but NOT boiling water Specimen should be sent in vials containing 70% ethanol. 7
Mosquito identification (adult specimen) Specimen killed with chloroform, ether, carbon dioxide or rapidly frozen in a domestic refrigerator The specimen should be packaged and sent in a small vial or cardboard box lined with grease-proof paper or paper towels. 7
Arbovirus detection in mosquitoes (Mosquito-based Surveillance) Adults sorted by species
Mosquito Eggs
Demonstration of the presence of Dengue viruses (1-4), Chikungunya virus, Zika virus, Western Equine Encephalitis virus, Yellow Fever virus, Mayaro, Ilheus, Bussuquara virus, Usutu virus, Spondweni virus, O'nyong nyong virus, Eastern Equine encephalitis virus, Semliki forest virus or Rocio virus in mosquitoes. 7