RITM Training Manual for

Specimen
Collection, Transport
and Referral during
Infectious Disease
Outbreak Response

MODULE 2: PLANNING AN OUTBREAK RESPONSE

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Learning Objectives
At the end of the presentation, participants can:

1. Define the possible causes of the outbreak

2. Decide which clinical specimens are required to confirm
the cause of the outbreak according to WHO syndromic
Surveillance

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Why Plan?
• Laboratory requirements relate to investigation of objectives
information (suspected agent: Bacterial, Viral or Parasitic)
Possibility of water and/or food-borne related source of pathogen
transmission
confirm a diagnosis to document an infection?
document a common source?
provide information to help clinical management (antibiotic resistance)?
• What laboratory tests help answer the objective(s)?
• What specimens are required for the laboratory test(s)?
• What’s the sampling strategy?
RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Organize a Team
• PIDSR Manual of Procedures states that the LGUs (Province/Municipal/City
Health Offices) shall organize multidisciplinary/multi-sectoral teams to
respond to events that may constitute a public health emergency like
outbreaks. The Epidemic Investigation and Control Team (EICT) should
include the following members:
• Outbreak Coordinator
• Surveillance Officer
• ESU staff
• Point of contact person from outbreak location (health care facility)
• Delegated government official
• Receiving Lab Manager
• Other(s) as required
RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Roles of the Team
• The Epidemic Investigation Control Team (EICT) will:
• Review and discuss expected roles of members and key contact
persons
• Coordinate needed logistics
• Set up information hubs to ensure that communications are clear
from the field to the laboratory or other concerned individuals or
agencies

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Session 1: Define the possible causes
of the Outbreak

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Recognizing potential outbreak causes
Define the possible causes of the outbreak
• An assessment of current clinical and epidemiological
information is the starting point for considering the potential
etiology of the outbreak.
• Since a variety of infectious agents can present with a similar
clinical picture, the outbreak should be approached in a
syndromic manner to obtain the differential diagnosis.
• One or more specimen types may now be required to define
the cause of the outbreak.

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Session 2: Syndromic Approach to Specimen
Collection , Transport and Referral

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
What is a syndrome?
a group of symptoms that consistently occur together
or a condition characterized by a set of associated
symptoms.
a symptom complex in which the symptoms and/or
signs coexist more frequently than would be expected
by chance on the assumption of independence.

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Syndromic Approach
• Methods relying on detection of clinical features
• Discernible before confirmed diagnoses are made
• Clustering of cases of ill persons
• Behavioral patterns, symptoms, signs, or laboratory findings
• Real-time nature
• Bioterrorism-related outbreak detection, monitoring and investigation
• Useful also for general public health and health programs

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Syndromic Approach
• Uses clinical features
• Describes onset of symptoms as an alert of changes
• Provides patient information from multiple existing sources
• ER consults
• OTC medication sales
• Must be integrated into the public health system
• Ensures a timely and adequate response

RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
When to use Syndromic Approach
• THINK of a syndrome where it could fit
• Definition – e.g. Acute neurologic syndrome
• Acute neurological dysfunction with one or more of the following:
deterioration of mental function, stupor/coma , acute paralysis, convulsion
signs of meningeal irritation e.g. neck stiffness,
involuntary movements e.g. myoclonus, tremors
other neurological symptoms e.g. headache, visual disturbances, vomiting AND severe illness

• Possible etiology or pathogen

• Specimens
• Laboratory tests
RITM Training Manual for Specimen Collection, Transport and Referral during
Infectious Disease Outbreak Response
Suspected
Acute Acute onset of respiratory distress AND absence of known predisposing factors
outbreak Respiratory
Syndrome Influenza Pertussis Bacterial pneumonia including:
Coronavirus Pneumococcal Respiratory Anthrax
Hantavirus
Possible (MERS,SARS) Legionellosis Pneumonic plague
pulmonary
diseases/pathogens Respiratory Syncytial Haemophilus Streptococcal
syndrome
virus (RSV) influenzae Pharyngitis and Scarlet fever
hMPV, ADV, EV) Mycoplasma Diphtheria

Sputum Blood Culture

Endotracheal Serum
Specimen Serum NPS/OPS aspirate Sputum
required Urine (for
Bronchial
washings Legionella)

Bacterial or Viral:
Laboratory Molecular Diagnostics
studies Serology
Culture (Viral and Bacterial)
 Acute
Suspected Acute diarrhoeal syndrome AND absence of known predisposing factors
Diarrhoeal
outbreak
Syndrome
Bacteria:
Shigellosis, Salmonellosis, Campylobacteriosis, Aeromonas, Plesiomonas, Cholera,
Possible Diarrheagenic E. coli, Clostridium difficile
diseases/pathogens Virus:
Rotavirus, Norovirus, Adenovirus, Ebola and other haemorrhagic fevers*
Parasite:
Giardiasis, Cryptosporidium, E. histolytica, other intestinal parasites

Specimen
Feces (rectal/fecal swab, fresh feces, preserved feces)
required

Bacterial: Viral: Parasite:

• Culture • Serology (Antigen • Direct Fecal Smear (DFS)
Laboratory • Formol Ethyl Acetate (FECT)
• Serology (Antigen detection)
studies • Modified Acid Fast (MAFT)
detection) • Polymerase chain reaction
• Antimicrobial susceptibility

*NOTE: For cases presenting bloody diarrhea, Ebola and other hemorrhagic fevers should be considered. Please refer to “Acute
Hemorrhagic Fever Syndrome” specimen collection guidelines.
 Acute onset of fever of less than 3 weeks duration AND any two of the following:
Acute
• Haemorhagic or purpuric rash
Suspected Haemorrhagic
• Epistaxis
outbreak Fever
• Haemoptysis
Syndrome
• Blood/stool
• Other haemorrhagic symptom
• AND absence of known predisposing factors.
Possible • Dengue haemorrhagic fever and shock syndrome
diseases/pathogens
• Yellow Fever
• Other arboviral haemorrhagic fevers (e.g. Rift Valley, Crimean Congo, Tick-borne
flaviviruses)
• Lassa fever and other arenaviral haemorrhagic fevers
• Ebola or Marburg haemorrhagic fevers
• Haemorrhagic fever with renal syndrome (hantaviruses)
• Malaria
• Relapsing fever
Serum
Specimen Post-mortem tissue specimens
Whole Blood Dried Blood spots
required Ante-mortem tissue
specimens
Viral:
Serology – IgG, IgM
Laboratory Immunochromatography Parasitic:
studies PCR Microscopy
Immunoflourescence PCR
Immunohistochemistry
*NOTE: Ebola and other hemorrhagic fevers may initially present as bloody diarrhea. If such an etiology is suspected, refer to “Acute Hemorrhagic Fever Syndrome” for appropriate
specimen collection guidelines.
Suspected Acute
Acute onset of conjunctivitis with or without sub-conjunctival haemorrhages AND absence
outbreak Ophthalmological
of known predisposing factors
Syndrome

Viral Infection:
Bacterial Infection:
Possible 1.Epidemic adenoviral
1.Chlamydia tachomatis
diseases/pathogens keratoconjunctivitis
2.Gonococcal
2. Haemorrhagic conjuctivitis
3.Other aerobic bacteria
(adeno- or enterovirus)

Specimen Conjunctival swab smear

required Conjunctival swab
Serum

1. Chlamydial:
(IF ELISA, PCR, Cell culture)
Viral:
Laboratory
2. Bacterial Infection: Cell culture
studies 2.1 Gram stain PCR
2.2 Culture
2.3 PCR
2.4 fluorescent treponemal antibody absorption
or Treponema pallidum particle agglutination
Suspected Acute Acute febrile illness with rash OR other skin manifestations
outbreak Dermatological AND absence of known predisposing factors
Syndrome*
Raseola
Chickenpox
Measles Bacterial infection
Possible Vesicular rash
Rubella Cutaneous anthrax
diseases/pathogens Erythema infectiosum
Typhus Streptococcus
(parvovirus B19)
Zika Staphylococcus
HFMD
ChikV

Specimen Serum Lesion swab

Vesicular Swab
required Urine (for Zika) Blood
CSF

PCR Culture
Laboratory
Serology(IgM) PCR
studies
Viral culture serology

* NOTE: The pathogens listed above reflect only those epidemic-prone conditions in which the principal manifestations may be
dermatological. Other common bacterial, fungal, parasitic, and viral conditions are not covered
Suspected Acute Jaundice Acute onset of jaundice AND absence of known predisposing factors
outbreak Syndrome

Possible Dengue Fever Leptospirosis and other

diseases/pathogens Yellow Fever
Hepatitis A/E spirochaetal diseases

Specimen Blood Culture

Post mortem liver Biopsy Serum
required (Urine*)

Viral: Leptospiral:
Hepa A/E:
1. Serology Anti-HAV IgM 1.Culture and PCR - (Whole
Laboratory 2. Serology Anti-HEV IgM blood, CSF, Urine, Serum)
studies Yellow Fever:
1.Post Mortem Liver Tissue Biopsy 2. Microscopic Agglutination Test
Dengue Fever: - (Serum)
1. Serology, PCR

* Requires specialized media and handling procedures

 Acute neurological dysfunction with one or more of the following:
• Detoriation of mental function
Suspected Acute • Acute paralysis
outbreak Neurological • Convulsions
Syndrome • Signs of meningeal irritation
• Involuntary movement
• Other neurological symptoms
Possible AND absence of predisposing factors
diseases/pathogens
Poliomyelitis or Guillain Viral, bacterial, fungal or parasitic
Rabies
Barre syndrome meningo-encephalitis

CSF , Blood, Urine, Tissue

Post mortem specimens (e.g.
Specimen Blood Smears
Faeces / Stool brain tissue, skin biopsy from
required Serum
neck, salivary gland)
Throat Swab

Bacterial (including leptospiral): Viral:

BACTERIA 1. Antigen Detection
Viral: 1. Aerobic Culture (Blood, CSF) Leptospiral Test1.1 dFAT (direct
culture (blood, urine, CSF and tissue) Flourescent Ab Test)
Virus isolation 2. Serology : 1.2 Direct rapid
Laboratory a. Bacterial Antigen Detection: whole blood, Immunohistochemistry Test
Real-time PCR serum, CSF, urine- (N.men, Spn, Hi) ; (DRIT)
studies Sequencing b. b. MAT for Leptospira (serum) 2. Ab Detection Test
3. PCR 2.1 Flourescent Antibody
a. Whole blood, CSF, serum (N. meningitidis, Virus Neutralization Test
S. pneumoniae, H. influenza) (FAVNT)
b. Leptospira spp.: Whole blood, CSF, serum, 2.2 ELISA
tissue 3. Realtime PCR