disase suerveillance

8/8/2019 DISASE SUERVEILLANCE

1/21

OutbreakSurveillanceand

Response

DiseaseEarlyWarningSystem

FloodingResponseinPakistan

OperationalGuidance

August2010


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TableofContents

I. Introduction

II. DiseaseEarlyWarningSystem

a) RiskAssessment

b) SettingupDEWS

c) Alert/Outbreakpreparedness,responseandcontrol

Annex1.Casedefinitionsfor2010floodingdisaster

Annex2:StandardDEWSreportingforms:Provincial,DistrictandHealthFacilitylevel

Annex3:AlertandOutbreakthresholdsforDEWS

Annex4:Alertinvestigationform

Annex5.Guidelinesforcollectionofspecimensinemergencyconditions


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I.Introduction

The recent floods in Pakistan have affected millions of people and greatly increased the risk of disease

outbreaks.ThisoperationalguidancewasdevelopedinordertostrengthensurveillanceusingtheDiseaseEarly

WarningSystem(DEWS),andtoallowacoordinatedapproachtodiseaseoutbreakpreparednessandresponse

inthefloodaffectedpopulations.TheDEWSsystemhasbeenfunctioning inPakistansince2005andhasrelied

on weekly reporting. The changes detailed in this document, including a daily reporting requirement, are a

temporary modification in response to the increased risk of outbreaks in the floodaffected populations. The

dailyreportingrequirementwillberelaxedastheriskofcommunicablediseasesdiminishes.

ThisdocumentwasdevelopedthroughtheNationalInfectiousDiseaseTaskForce,withsupportfromtheWorld

HealthOrganization.Thepurposeof this document is to provideastandardizedapproach tosurveillanceand

responsetoepidemicpronediseases inthe floodaffectedareasofPakistan.Wehopethat theplanmayalso

provideaframeworkforcoordinatedresponsetootherepidemicsandpublichealthemergencies.

II.DiseaseEarlyWarningSystem

Theeffectivenessofcommunicablediseasecontrolduringemergencies reliesonacomprehensive and robust

diseasesurveillancesystem.Asensitivecommunicablediseasesurveillance/earlywarningandresponsesystem

should be established at the beginning of public health activities set up in response to an emergency. The

surveillancesystemshouldbesimple,flexible,situationspecificandwidelyaccepted.

The Disease Early WarningSystem (DEWS) is a program by which health care workers can detect signs of an

epidemicatanearlystageinordertorapidlyrespondandtolimittheimpact.DEWSwasfirstsetupin2005in

Pakistaninresponsetotheearthquakecrisis,andhassincebeenexpandedtootheremergencyaffectedareasin

Pakistan.Currently,

DEWS

is

expanding

into

the

areas

affected

by

the

2010

flooding

disaster.

TheoverallgoalofDEWSistominimizemorbidityandmortalityduetocommunicablediseases.Theobjectiveis

todetectpotentialoutbreaksatitsearliestpossiblestageandtofacilitatetimelyinterventions.

Disease early warning for rapid detection and prompt response to outbreaks is one of the priorities during a

humanitariancrisis,ascommunicablediseasescanbeamajorcauseofmorbidityandmortalityinemergencies.

The following document presents guidance for the implementation of DEWS in the flood affected areas of

Pakistan.

a. Risk Assessment

Theaimoftheriskassessment isto identifythemaincommunicablediseasethreats,outlinethepublichealth

needsandplanpriorityinterventions.Otherimportantobjectivesoftheriskassessmentaretoassesstheextent

of communicable disease risk and threats of outbreaks, and to define the type and size of interventions and

priorityactivitiesneeded.

ThefloodaffectedareasofPakistanareathighriskofwaterbornediseases(acutewaterydiarrhea,HepatitisA

and E, shigellosis, and typhoid), diseases associated with overcrowding (measles and meningitis), and vector

bornediseasessuchasmalariaanddengue.


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b. Setting up DEWSThe following steps should be followed in setting the surveillance system in the flood affected areas of

Pakistan.

(i)SettingsurveillanceprioritiesIt is not possible to monitor everything in an emergency. In coordination with the health partners and local

healthauthoritiesa limitednumberofprioritycommunicablediseasesthatposeathreat tothehealthofthe

population have been identified. Experience from many emergency situations has shown that certain

diseases/syndromesmustbeconsideredasprioritiesandmonitoredsystematically.Inthefloodaffectedareas

ofPakistan,thefollowingdiseases/syndromesareepidemicproneanddeemedaspriorityillnesses:

Acutewaterydiarrhea Bloodydiarrhea AcuteRespiratoryInfection AcuteFlaccidParalysis SuspectedMeasles AcuteJaundiceSyndrome SuspectedMalaria SuspectedMeningitis SuspectedHaemorrhagicFever UnexplainedFever>38.5C Unexplainedclusterofhealthevents Otherdiarrhealdiseases

(ii)StandardCaseDefinitionsStandardoperationalcasedefinitionsmustbeusedbyallhealthproviderstoensureconsistency(SeeAnnex1).

Thesearesurveillancecasedefinitionsusedtoclassifycasesforreporting.

(iii) PlanningandImplementation:DEWSshouldaimtoincludeallhealthfacilities,hospitals,andhealthcareprovidersinthefloodaffectedareas.

Thesurveillanceactivitiesshouldnotbelimitedtosentinelsitesonly.

Identifythehealthfacilities,hospitals, andmobilemedicalteamstoincludeasreportingsites Identifyaresponsiblefocalpersonineachhealthfacility/reportingsite

(iv) DataCollectionandReportingThe DEWS focal point at each reporting site must be oriented on the use of the form. DEWS reporting must

capturethe

following

categories

of

health

related

parameters:

Morbidity(illness)mortality(deaths),bothdisaggregatedbyage(5years).

DEWSsurveillanceisexhaustive,andaimstoincludeeverypatientinteractionoccurringinthefloodaffectedareas.

Atpresent,promptdaily reporting (including zero reporting) is required. The standard DEWS reportingformsshouldbeusedateachrespectivelevel(seeAnnex2).

Thereportingdayendsat3:00pm.Patientsseenafter3:00pmshouldbereportedthefollowingday.


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Eachdayat4:00pm,theinformationfromeachreportingsite(healthfacility,mobileclinic,privatepractices,NGOclinics,etc.)shouldbecompiledandtheHealthFacilityFormcompleted(SeeAnnex2).

By4:00pmthe formshouldbesent from the reportingsitetothedistrict level (ExecutiveDistrictOfficerHealth, or District Surveillance Coordinator) where reports will be reviewed, compiled, analysed, and

appropriateactiontakenasnecessary.TheDistrictReportingFormmustbecompleteddailyateachdistrict. From district level the compiled daily data should be sent by 6:00 pm to the provincial level (Provincial

SurveillanceOfficer)

and

to

the

central

level

for

compilation

and

further

analysis.

The

ProvincialReportingFormmustthenbecompletedattheprovinciallevel.

Fromtheprovincial levelthedatawillbecompiledandsenttothecentral levelby10:00amthefollowingdayforanalysisandinclusioninthedailybulletintobeissuedat4:00pm(SeeFigure1).

Technicalsupervisionandsupportforflowof informationfromthefieldshouldbeprovidedatthedistrict,provincialandcentrallevels.

DEWSreportingstandardsateachlevel

Healthfacilityfocalpoint:

Reportingperiodis3:00pm 3:00pm.Reviewtheregisterandmedicalrecordsofpatientsseenbythefacilityduringthisperiodeachday.

CompletetheHealthFacilityReportingFormandsendtotheDistrictSurveillanceCoordinatorby4:00pmdaily.

DistrictSurveillanceCoordinator:

Receivereportsfromthehealthfacilitiesbeginningat4:00pm. CompletetheDistrictReportingFormandsendtotheProvincialSurveillanceOfficerandCentrallevelDEWS

coordinatorby6:00pmdaily.

Reviewandanalysethereceiveddata,andchecktoseeifalertthresholdshavebeencrossed. Verifyalerts,initiateoutbreakinvestigationsasnecessary.

ProvincialSurveillanceOfficer:

Receivereportsfromthedistrictsbeginningat6:00pm. CompletetheProvincialReportingFormandsendtotheCentrallevelDEWScoordinatorby10:00amthe

nextday.

ReviewandanalysethereceiveddataforinclusionintheProvincialepidemiologicalbulletin. Providetechnicalandoperationalsupportforoutbreakresponseasneeded.

CentrallevelDEWScoordinator:

Receivereportsfromtheprovincesanddistrictsbeginningat10:00am. ReviewandanalysethereceiveddataforinclusionintheEpiBulletin,tobepublishedby4:00pmdaily. Providetechnicalandoperationalsupportforoutbreakresponseasneeded.


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Figure1.FlowofinformationandtimingofreportsforDEWSinfloodaffectedareasofPakistan

(v)Dataanalysis,interpretationandfeedbackThebasicdataanalysismustbedoneatthefieldlevelbytheDistrictSurveillanceCoordinators.Thedataisthen

forwardedtotheprovinciallevelandthentothecentrallevelforfurtherinterpretation,analysisandfeedback.

In the initial stages of an emergency, the most important data elements to be analyzed are the number of

illnessesanddeaths,thelocationoftheseevents,andthecomparisontousualdiseasetrends.

DistrictSurveillanceCoordinators/SurveillanceOfficers

Review,analyzeandrespondtothealertsondailybasis,withassistancefromRapidResponseTeams. Providetechnicalguidanceonpublichealthinterventionsneededtocontrolthecommunicablediseases. Provide feedback to reporting sites to keep them motivated for regular reporting and inform about main

healthproblemsinthearea.

Sharetheinformationwiththedecisionmakersforpolicydecisionsandresourcemobilization.

c. Alert / outbreak preparedness, response and control

Alertsareunusualhealtheventsthatsometimessignaltheearlystagesofanoutbreak.Alertsmustbequickly

detectedandinvestigated.TheaimoftheDEWSistodetectanoutbreakasearlyaspossibleandtocontrolthe

spreadofdiseaseamongthepopulationatrisk.WithDEWS,alertthresholdscanallowearlydetectionofthreats

Central

District

Province

Health

Facility

Health

Facility

Health

Facility

Health

Facility

Health

Facility

HealthFacilitiesreportingby4:00pmsameday

Districtsreportingby4:00pmsameday

Provincesreportingby10:00amnextday

PatientsseenatHealthFacilities

EpiBulletinpublished

by

4:00

pm

next

day

Feedbackfromeachlevel


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ofpotentialoutbreaks.

Outbreakscanspreadveryrapidlyinemergencysituationsandmayleadtohighratesofmorbidityand

mortality.Outbreakscanseverelystrainthehealthsystem,andfrequentlyexpandbeyondthehealthsectorto

becomemultisectoral.Coordinationamongsectorsiscrucialtoensureacomprehensiveandeffectiveresponse.

Stepsinthemanagementofacommunicablediseaseoutbreaka. PreparednessOutbreak preparedness is essential to respond most effectively to outbreaks. Key components include a

multisectoraloutbreakcontrolteam;anoutbreakresponseplan;standardtreatmentprotocolsforkeydiseases,

withtrainingofclinicalworkers;stockpilesofessentialtreatmentsupplies (medicationandmaterial,e.g.,oral

rehydrationsalts, intravenousfluids,vaccinationmaterial,personalprotectiveequipment,transportmediaand

water purification supplies); laboratory sampling kits for the priority diseases and a competent laboratory

identifiedforconfirmationofcases;andpreidentificationofsitesforisolationorsurgepatientcapacity.

Focusedsurveillance:dailyDEWS reporting fromall thehealth/reportingunits andhealth partners to theMoH/WHO

Outbreakresponseplansforeachprioritizeddisease,includingresources,skillsandactivitiesneeded. Sample collection and transportation kits, appropriate antimicrobial, intravenous fluids, vaccines,

disinfectantsetc.,shouldbestockpiled.

b. DetectionDEWSprovidesanearlywarningmechanismforrapiddetectionofkeyepidemicpronediseases.Byusingalert

thresholds foreachdisease,outbreaksanddiseaseeventscanbequicklydetectedtoallowrapid investigation

andresponse.

Alert thresholds and actions needed for each of the priority communicable disease have been defined (see

Annex3).Insituationswherethealertthresholdispassed,theDistrictSurveillanceofficerandExecutiveDistrict

Officer

Health

should

be

informed

as

soon

as

possible;

the

health

coordinator

should

inform

the

Ministry

of

HealthandWHO.AlertsshouldbeinvestigatedusingtheAlertInvestigationForm(SeeAnnex4).c. Response

i. Confirmation

TheDistrictSurveillanceofficerinvestigatesreportedalertstoverifytheirvalidityandassessthelikelihoodof

anoutbreak.Clinicalspecimenscanbecollectedandsentforlaboratorytesting(SeeAnnex5)asrequired.

ii. Investigation

Investigationofoutbreaksshouldbeinitiatedatdistrictlevel,withsupportasnecessaryfromdistrictresources

(Executive

District

Officer

Health

office,

Rapid

Response

Team,

District

Emergency

Preparedness

and

Response

Unit), provincial resources (Provincial Director General Health office, Provincial Emergency Preparedness and

ResponseUnit),orcentral levelresources(EpidemicInvestigationCell,NationalInfectiousDiseasesTaskForce,

FELTP).

Thestepsinvolvedinoutbreakinvestigationaresummarizedbelow.Thestepsoftendonothappeninsequence,

andoutbreakcontrolmeasuresshouldbe implementedassoonaspossible.Inthe initialstageofanoutbreak,

thecausativeagentmaynotbeknownandgeneralcontrolmeasuresmaybetakenbasedonthebestavailable

data.Oncethecauseisconfirmed,specificmeasures(e.g.,vaccination)canbeundertaken.


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a) Establishtheexistenceofanoutbreak Aretheinitialreportsverified?Hasthethresholdbeencrossed?

b) Confirmthediagnosis Laboratoryinvestigationtoconfirmclinicalimpressions;personallyexaminecasesifpossible

c) Defineacase Thesymptomsincludedintheoutbreakcasedefinitionmustbesimpleandeasilyapplied,and mustbalancesensitivityandspecificity

d) Countcases Casefindingandlinelistingofcases,toestablishtheextentoftheoutbreak(SeeAnnex4)

e) Performdescriptiveepidemiology(time,person,place)anddevelopanepidemiccurve Determinewhoisatriskandwhere

f) Develophypothesesexplainingexposure&disease Sourceoftheoutbreak?Modeoftransmission? oftenobviousfromdescriptiveepidemiology

g) Implementcontrolmeasuresassoonaspossible May change from general measures to specific measures as the investigation progresses and the

epidemiologyisrefined

h) Evaluatehypotheses

Formal

epidemiological

studies

may

be

needed

to

further

define

risk

and

refine

control

methods

i) Communicatefindings Communicatepublichealthmessages Preparewrittenreport

AnOutbreakControlTeam(OCT)whichrepresentsarangeofskillsandstakeholders isacriticalcomponentof

aneffectiveoutbreakresponse.

iii. Control:commonlyusedinterventionstosupportoutbreakcontrol

Interrupt environmental sources (safe water, sanitation, adequate shelter, standard infection controlprecautions

in

health

care

facilities)

Removepersonsfromexposure(influenzaandsocialdistancingmeasures) Modifyhostresponse(vaccination,treatmentofcases,prophylacticchemotherapy) Inactivate/neutralizethepathogen(watertreatmentmeasures) Isolateinfectedpersons(VHF,cholera) Controlvectortransmission(IRS,larvicide,environmentalhygiene dependingonlocalvectorspecies) Improvepersonalhygiene(healtheducation,soap) Removesourceofcontamination(intoxication).

iv. Evaluation

Assesstimelinessofoutbreakdetectionandresponse. Assessappropriatenessandeffectivenessofcontrolmeasures. Informpublichealthpolicy. Writeanddisseminateoutbreakreport.


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Annex1.DEWSsurveillancecasedefinitionsfor2010floodingdisaster

ACUTEWATERYDIARRHEA

Inanareawherecholeraisnotknowntobepresent:apersonaged>5yearswithseveredehydrationordeath

fromacutewaterydiarrhoeawithorwithoutvomiting.

Inanareawherethereisacholeraoutbreak: apersonaged>5yearswithacutewaterydiarrhoeawithorwithoutvomiting.Toconfirmacaseofcholera:

IsolationofVibriocholeraO1orO139fromadiarrhoealstoolsample.BLOODYDIARRHOEA

Acutediarrhoeawithvisiblebloodinthestool.

Toconfirmacaseofepidemicbacillarydysentery:takeastoolspecimenforcultureandbloodforserology;

isolationofShigelladysenteriaetype1.OTHERDIARRHOEA

Acutediarrhoea(passageof3ormoreloosestoolsinthepast24hours)withorwithoutdehydration,andwhichis

notduetobloodyorwaterydiarrhea.

ACUTEFLACCIDPARALYSIS(SUSPECTEDPOLIOMYELITIS)

Acuteflaccidparalysisinachildaged


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Note:Severepneumonia=coughordifficultybreathing+oneormoreofthefollowing(inabilitytodrinkorbreastfeed,severevomiting,convulsions,lethargyorunconsciousness)orchestindrawingorstridorina

otherwisecalmchild

MALARIA

Personwithcurrentfeverorhistoryoffeverwithinthepast48hours(withorwithoutothersymptomssuchas

nausea,vomiting

and

diarrhoea,

headache,

back

pain,

chills,

muscle

pain)

with

positive

laboratory

test

for

malariaparasites(bloodfilm(thickorthinsmear)orrapiddiagnostictest).

InchildrenUncomplicatedmalaria

FeverANDnogeneraldangersignssuchaslethargyorunconsciousness,convulsions,orinabilitytoeatordrink.

Wherepossible,confirmmalariawithlaboratorytest.

Severemalaria

FeverANDgeneraldangersigns(lethargyorunconsciousness,convulsions,orinabilitytoeatordrink).

MEASLES

Feverandmaculopapularrash(i.e.nonvesicular)andcough,coryza(i.e.runnynose)orconjunctivitis(i.e.red

eyes)orAnypersoninwhomaclinicalhealthworkersuspectsmeaslesinfection.

Toconfirmacaseofmeasles:

PresenceofmeaslesspecificIgMantibodies.

MENINGITIS

Suspectedcase:Suddenonsetoffever(>38.5C)withstiffneck.In

patients

aged

38.5C)for>48hoursandwithoutotherknownetiology.

UNEXPLAINEDCLUSTEROFHEALTHEVENTS

Anaggregationofcaseswithsimilarsymptomsandsignsofunknowncausethatarecloselygroupedintime

and/orplace.


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Annex2:StandardDEWSreportingforms: Provincial,DistrictandHealthFacilitylevel________________________________________________________________________

PakistanFlood2010

DEWSDaily

Reporting

Form

ProvincialReportingForm

Province:______________Date:___/___/2010 Totalpopulationundersurveillanceonthedayof

reporting:_________________

Totalnumberoffunctioningreportingsitesintheprovince

Numberofsitesreported

Totalnumberofmobilemedicalteams/campsintheprovince Numberofmobilemedicalteams/campsreported

Disease Cases Deaths 5yrs 5yrs

AcuteWateryDiarrhea

BloodyDiarrhea

OtherDiarrhea

AcuteRespiratoryInfection

AcuteFlaccidParalysis

SuspectedMeasles

AcuteJaundiceSyndrome

SuspectedMalaria

SuspectedMeningitis

SuspectedHaemorrhagicfever

UnexplainedFever>38.5C

Unexplained cluster of

healthevents

Others(includingskindiseases)

Total


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PakistanFlood2010

DEWSDailyReportingForm

DistrictReportingForm

Province:______________ District:___________________ Date:___/___/2010 Totalpopulationundersurveillanceonthedayof

reporting:_________________

Totalnumberoffunctioningreportingsitesinthedistrict Numberofsitesreported

Totalnumberofmobilemedicalteams/campsinthedistrict Numberofmobilemedicalteams/campsreported


AcuteWateryDiarrhea

BloodyDiarrhea

Other

Diarrhea



SuspectedMeasles


SuspectedMalaria

SuspectedMeningitis

SuspectedHaemorrhagic

fever



healthevents


Total


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PakistanFlood2010

DEWSDailyReportingForm

HealthFacilityForm

Province:_________________ District:____________________ Date:____/____/2010_________ HealthfacilitynameandType(fix/Mobile)______________________Location:_________________CatchmentPopulation:____________________Reportedby:_____________________________ ContactNumber:__________________________


AcuteWateryDiarrhea

BloodyDiarrhea

OtherDiarrhea



Suspected

Measles


SuspectedMalaria

SuspectedMeningitis

SuspectedHaemorrhagic

fever



healthevents


Total


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Annex3:Alertthresholdstotriggerfurtherinvestigation

Disease/Condition AlertThreshold Actionsuggested

AcuteWateryDiarrhea Onesuspectedcase Reinforceappropriatecasemanagement;initiate

investigation

BloodyDiarrhea Threeormorecasesinone

location

Reinforceappropriatecasemanagement,

includingantibioticusage;collectstoolforculture

andantimicrobialsensitivity;initiateinvestigation

AcuteRespiratoryInfection Twicetheaveragenumberof

casesseeninthepreviousthree

weeksforagivenlocation

Reinforceappropriatecasemanagement;initiate

investigation

AcuteFlaccidParalysis Onesuspectedcase Caseinvestigation andspecimencollectionfor

laboratorydiagnosis

SuspectedMeasles Onecase Immediateinvestigation andactivecasefindingin

coordinationwiththenationalimmunization

programme

AcuteJaundiceSyndrome Threeormorecasesinone

location

Initiateverificationandinvestigationasrequired.

Specimencollectionforlaboratoryconfirmation

SuspectedMalaria Twicethemeannumberofcases

seeninthepreviousthreeweeks

foragivenlocation

Activefeverfindingandspecimencollectionfor

laboratoryconfirmation

SuspectedMeningitis Onecase Reinforceappropriatecasemanagement;initiate

investigation

AcuteHaemorrhagicFever

syndrome

Oneprobablecase Initiateverificationandinvestigationasrequired

UnexplainedFever Onedeathortwotimesthemean

numberofcasesoftheprevious

threeweeksforagivenlocation

Initiateinvestigation

Unknowndiseases

occurringincluster

Anaggregation

of

cases

with

relatedsymptomsandsignsof

unknowncausethatareclosely

groupedintimeand/orplace

Initiateverification

and

investigation

as

required.


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Annex4.AlertInvestigationForm

District/Area: Town/Village/Settlement/Camp: .

Health Facility: . Agency: .

Date: //.

Name of reporting officer: ..

Suspected disease/ syndrome:

(tick one box only)

Symptoms and signs:

(you can tick several boxes)

o Suspect cholerao Acute diarrhoeao Bloody diarrhoeao

Acute Jaundice Syndromeo Suspected meningitiso Acute Respiratory Infectiono Suspected measleso Unexplained fevero Suspected malariao Acute Haemorrhagic Fever

Syndrome

o Cluster of cases or deaths ofunknown origin

o Acute flaccid paralysis /suspectedpoliomyelitis (AFP)

o Other

o Acute watery diarrhoeao Acute diarrhoeao Bloody diarrhoeao Fevero Rasho Other skin lesiono Cougho Vomitingo Jaundiceo Neck stiffnesso Convulsions/Seizureso Muscle weaknesso Increased secretions (e.g. sweating, drooling)o Altered level of consciousnesso Other (specify):_____________________________________

TOTAL NUMBER OF CASES REPORTED:

Line listing

Case

No.

Age Address Sex

(M/F)

Dateof

onset(dd/mm/YY)

Lab

specimen

taken

Treatment

given(Yes/No)

Outcome Final

diagnosis

Epi

linked?(Yes/No)

Laboratory specimens: B=Blood, S=Stool, C=CSF, U=Urine, O = other Outcome: I = Currently ill, R= Recovering or recovered, D = d Known contact with previously identified case (list case no.)


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Annex5.Guidelinesforcollectionofspecimensinemergencyconditions

A.BLOODSPECIMENCOLLECTION

Bloodandseparatedserumarethemostcommonspecimenstakeninoutbreaksofcommunicabledisease.

Venousbloodcanbeusedforisolationandidentificationofthepathogenincultureandbyinoculation, or

separatedintoserumforthedetectionofgeneticmaterial(e.g.bypolymerasechainreaction),specific

antibodies(byserology),antigensortoxins(e.g.byimmunofluorescence).Fortheprocessingofmostspecimens

fordiagnosisofviralpathogens,serumispreferabletounseparatedbloodexceptwhereotherwisedirected.

Whenspecificantibodiesarebeingassayed,itisoftenhelpfultocollectpairedsera,i.e.anacutesampleatthe

onsetofillnessandaconvalescentsample14weekslater.Wheneverpossible,bloodspecimensforculture

shouldbetakenbeforeantibioticsareadministeredtothepatient.

Venousbloodsamples

MaterialsforcollectionSkindisinfection:70%alcohol(isopropanol,ethanol)or10%povidoneiodine,swabs,gauzepads,

adhesivedressings.

Disposablelatexorvinylgloves.

Tourniquet,Vacutainerorsimilarvacuumbloodcollectiondevices,ordisposablesyringesandneedles.

Vacutainer

or

sterile

screw

cap

tubes

(or

cryotubes

ifindicated),

blood

culture

bottles

(50

ml

for

adults,

25

ml

forchildren)withappropriatemedia.

Labelsandindeliblemarkerpen.

MethodofcollectionFullinfectioncontrolmeasuresmustbetaken,withgowns,gloves,masksandbootsforsuspectedviral

haemorrhagicfeversuchasLassafeverorEbola.

Place

a

tourniquet

above

the

venepuncture

site.

Disinfect

the

tops

of

blood

culture

bottles.

Palpateandlocatethevein.Thevenepuncturesitemustbemeticulouslydisinfectedwith10%povidoneiodine

or70%alcoholbyswabbingtheskinconcentricallyfromthecentreofthevenepuncturesiteoutwards.Letthe

disinfectantevaporate.Donotpalpatetheveinagain.Performvenepuncture.

Ifusingconventionaldisposablesyringes,withdraw510mlofwholebloodfromadults,25mlfromchildren

and0.52mlfrominfants.Usingaseptictechnique,transferthespecimentotheappropriatecaptransport

tubesandculturebottles.Securecapstightly.


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Ifusingavacuumsystem,withdrawthedesiredamountofblooddirectlyintoeachtransporttubeandculture

bottle.

Removethetourniquet.Applypressuretositeuntilbleedingstops,andapplydressing.

Labelthetube,includingtheuniquepatientidentificationnumber,usingindeliblemarkerpen.

Donotrecapusedsharps.Discarddirectlyintothesharpsdisposalcontainer.

Completethecaseinvestigationandthelaboratoryrequestformsusingthesameidentificationnumber.

HandlingandtransportBloodspecimenbottlesandtubesshouldbetransporteduprightandsecuredinascrewcapcontainerorina

rackinatransportbox.Theyshouldhaveenoughabsorbentpaperaroundthemtosoakupalltheliquidincase

ofspill.

For

serum

samples

(e.g.

measles,

yellow

fever,

HIV),

the

blood

cells

must

be

separated

from

serum.

Let

the

clot

retractfor30minutesthencentrifugeat2000rpmfor1020minutesandpouroffserum.Ifnocentrifugeis

available,placesampleinrefrigeratorovernight(46hours)andpourofftheserumfortransportinacleanglass

tube.

Donotattemptthisincaseofsuspectedviralhaemorrhagicfeverunlessyouareaclinician/laboratory

technicianexperiencedinmanagementofthedisease.Fullprotectionandinfectioncontrolmeasuresmustbe

taken.

Ifthespecimenwillreachthelaboratorywithin24hours,mostpathogenscanberecoveredfromblood

culturestransportedatambienttemperature.Keepat48Cforlongertransitperiods,unlessthebacterial

pathogenis

cold

sensitive.

B.FAECALSPECIMENCOLLECTION

Stoolspecimensaremostusefulformicrobiologicaldiagnosisifcollectedsoonafteronsetofdiarrhoea(for

viruses


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Parasitologytransportpack:10%formalin,polyvinylisopropylalcohol(PVA).

Methodofcollectingastoolspecimen

IfCaryBlairtransportmediumisavailable:

Placesterileswabinfreshlypassedstooltoallowitsoakupstool.

PlaceswabintheCaryBlairtransportmediuminsidethetube.

Breakoffthetoppartofthestickwithouttouchingthetubeandtightenthescrewcapfirmly.

Labelthespecimentube.

IfCARYBLAIRtransportmediumisnotavailable,collectfreshlypassedstool,5mlliquidor5gsolid(peasize),in

acontainer.Labelthecontainer.

Methodofcollectingarectalswabfrominfants

Moisten

aswab

in

sterile

saline.

Inserttheswabtipjustpasttheanalsphincterandrotategently.

Withdrawtheswabandexaminetoensurethatthecottontipisstainedwithfaeces.

Placetheswabinsteriletube/containercontainingtheappropriatetransportmedium.


Labelthespecimentube.

Handlingandtransport

Stoolspecimensshouldbetransportedinacoldboxat48C.Bacterialyieldsmayfallsignificantlyif

specimensarenotprocessedwithin12daysofcollection.Shigellaisparticularlysensitivetoelevatedtemperatures.Iftransportmediumisnotavailable,donotallowspecimentodryaddfewdropsof0.85%

sodiumchloridesolution.

Specimenstobeexaminedforparasitesshouldbemixedwith10%formalinorPVA,3partsstoolto1part

preservative.Transportedatambienttemperatureincontainerssealedinplasticbags.

C.RESPIRATORYTRACTSPECIMENCOLLECTION

Specimensarecollectedfromtheupperorlowerrespiratorytract,dependingonthesiteofinfection.Upper

respiratorytractpathogens(viralandbacterial)arefoundinthroatandnasopharyngealspecimens.Lower

respiratorytractpathogensarefoundinsputumspecimens.FororganismssuchasLegionella,cultureisdifficult,

anddiagnosisisbestbasedonthedetectionofantigenexcretedintheurine.Whenacuteepiglottitisis

suspected,noattemptshouldbemadetotakethroatorpharyngealspecimenssincetheseproceduresmay


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precipitaterespiratoryobstruction.EpiglottitisisgenerallyconfirmedbylateralneckXray,buttheetiological

agentmaybeisolatedonbloodculture.

Materialsforcollection

Transportmediabacterial(TransAmies)andviral(Cellmatics)

Dacronandcottonswabs

Tonguedepressor

Flexiblewirecalciumalginatetippedswab(forsuspectedpertussis)

Nasalspeculum(forsuspectedpertussisnotessential)

Suctionapparatusor2050mlsyringe

Sterilescrewcaptubes,andwidemouthedcleansterilejars(minimumvolume25ml).

Upperrespiratorytractspecimens

MethodofcollectingathroatswabHoldthetonguedownwiththedepressor.Useastronglightsourcetolocateareasofinflammationand

exudateintheposteriorpharynxandthetonsillarregionofthethroatbehindtheuvula.

RubtheareabackandforthwithaDacronorcalciumalginateswab.Withdrawtheswabwithouttouching

cheeks,teethorgumsandinsertintoascrewcaptubecontainingtransportmedium.


Label

the

specimen

containers.

Completethelaboratoryrequestform.

Methodofcollectingnasopharyngealswabs(forsuspectedpertussis)Seatthepatientcomfortably,tilttheheadbackandinsertthenasalspeculum.

Insertaflexiblecalciumalginate/Dacronswabthroughthespeculumparalleltothefloorofnosewithout

pointingupwards.Alternatively,bendthewireandinsertitintothethroatandmovetheswabupwardsinto

thenasopharyngealspace.

Rotatetheswabonthenasopharyngealmembraneafewtimes,removeitcarefullyandinsertitintoascrew

captube

containing

transport

medium.


Labelthespecimentube,indicatingleftorrightside.


Repeatontheotherside.

Lowerrespiratorytractspecimens


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MethodofcollectingsputumInstructpatienttotakeadeepbreathandcoughupsputumdirectlyintoawidemouthedsterilecontainer.

Avoidsalivaorpostnasaldischarge.Minimumvolumeshouldbeabout1ml.

Labelthespecimencontainer.


HandlingandtransportAllrespiratoryspecimensexceptsputumaretransportedinappropriatebacterial/viralmedia.

Transportasquicklyaspossibletothelaboratorytoreduceovergrowthbycommensaloralflora.

For

transit

periods

up

to

24

hours,

transport

bacterial

specimens

at

ambient

temperature

and

viruses

at

48

C

inappropriatemedia.

D.URINESPECIMENCOLLECTION

Materialforcollection

Sterileplasticcupwithlid(50mlormore).

Clean,

screw

top

specimen

transport

containers

("universal"

containers

are

often

used).

Gauzepads.

Soapandcleanwater(ornormalsaline)ifpossible.

Labelsandindeliblemarkerpen.

Methodofcollection

Givethepatientclearinstructionstopassurineforafewseconds,andthentoholdthecupintheurinestream

forafewsecondstocatchamidstreamurinesample.Thisshoulddecreasetheriskof

contaminationfromorganismslivingintheurethra.

Todecreasetheriskofcontaminationfromskinorganisms,thepatientshouldbedirectedtoavoidtouching

theinsideorrimoftheplasticcupwiththeskinofthehands,legsorexternalgenitalia.Tightenthecapfirmly

whenfinished.

Forhospitalizedordebilitatedpatients,itmaybenecessarytowashtheexternalgenitaliawithsoapywaterto

reducetheriskofcontamination.Ifsoapandcleanwaterarenotavailable,theareamayberinsedwithnormal

saline.Drytheareathoroughlywithgauzepadsbeforecollectingtheurine.


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Urinecollectionbagsmaybenecessaryforinfants.Ifused,transferurinefromtheurinebagtospecimen

containersassoonaspossibletopreventcontaminationwithskinbacteria.Useadisposabletransferpipetteto

transfertheurine.

Labelthespecimencontainers.

Handlingandtransport

Transporttothelaboratorywithin23hoursofcollection.Ifthisisnotpossible,donotfreezebutkeepthe

specimenrefrigeratedat48C.Keepingthespecimenrefrigeratedwillreducetheriskofovergrowthof

contaminatingorganisms.

Ensurethattransportcontainersareleakproofandtightlysealed.

disase suerveillance

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