Table 2

Pathogen-based diagnostic testing for the Febrile Illness Evaluation in a Broad Range of Endemicities (FIEBRE)

Infection or pathogen soughtSample typeDiagnostic testNotes
Pathogen-based diagnostic tests to be performed at or near the point of care
 Malaria (Plasmodium species)EDTA whole bloodAntigen-detecting lateral flow malaria rapid diagnostic test (mRDT)Combination test detects histidine-rich protein 2 and Plasmodium lactate dehydrogenase
Thick and thin blood smearExpert light microscopy for the presence versus the absence of asexual parasites, species and densityFor all mRDT-positive samples and 10% of mRDT-negative samples
 HIV*EDTA whole bloodAntibody-detecting rapid tests according to national guidelinesConfirmatory molecular testing according to national guidelines for infants who test antibody-positive
 Bacteraemia and/or fungaemiaWhole bloodAerobic culture, identification and antimicrobial susceptibility testing performed for isolated microorganismsSingle culture bottle; blood volume of ≤10 mL, weight-based volumes for small children
 Mycobacteraemia*Whole bloodMycobacterial cultureFor patients aged ≥15 years who are HIV-infected and/or admitted as inpatients
Mycobacterium tuberculosisUrineUrinary lipoarabinomannan rapid testFor patients who are HIV-infected and/or admitted as inpatients
Cryptococcus speciesSerumAntigen-detecting lateral flow rapid diagnostic testFor patients who are HIV-infected and/or admitted as inpatients
 Nitrites and leucocyte esterase (evidence of urinary tract infection)UrineUrine dipstickUrine culture performed on samples positive for nitrites and/or leucocyte esterase
 BacteriuriaUrineCulture, identification and antimicrobial susceptibility testing performed for isolated microorganismsFor samples dipstick-positive for nitrites and/or leucocyte esterase
External quality assessment of diagnostic results obtained at or near the point of care, to be performed at internationally recognised reference laboratories
 Malaria (Plasmodium species)Thick and thin blood smearExpert light microscopy for the presence versus the absence of asexual parasites, species and densityRandomly selected sample of 10% of microscopy-positive and 10% of microscopy-negative smears from each site
 Bacteria and fungi isolated from blood and urine at sitesCryopreserved isolatesMALDI-TOF MS for identification and drug susceptibility testing to EUCAST standards
 Mycobacteria isolated from blood at sitesCryopreserved isolatesIdentification using subculture and molecular testing, drug susceptibility testing depending on organisms identified
Pathogen-based diagnostic tests to be performed at internationally recognised reference laboratories
Borrelia species (louse-borne and tick-borne relapsing fevers)Thick and thin blood smearExpert light microscopyRandom 10% sample of all smears from each site; if positives are identified, a larger proportion are to be read
 Arboviruses: chikungunya, dengue, Japanese encephalitis, o’nyong ‘nyong, ZikaSerumAfrica-specific or Asia-specific IgG ELISA and qPCR, microneutralisation for samples positive by ELISAA proportion of African samples to be tested for Japanese encephalitis virus, and a proportion of Asian samples to be tested for o’nyong ‘nyong virus; if positives are identified, a larger proportion of samples are to be tested
Brucella species (brucellosis)SerumBrucella IgM EIA, Brucella microagglutination test for samples positive by EIAConvalescent sera screened for exposure using EIA; positives tested by IgM EIA and microagglutination on acute and convalescent sera
Leptospira species (leptospirosis)SerumMicroagglutination test
 Rickettsiae: Orientia species, Rickettsia (typhus group and spotted fever group), Coxiella burnetiiSerum and buffy coatIgG and IgM IFA; qPCRfor samples positive by serological screenBuffy coat is preferred sample for Orientia and rickettsial species detection, serum to be used for C. burnetii
 Visceral leishmaniasisSerumDirect agglutination test
Histoplasma species (histoplasmosis)SerumHistoplasma EIA††
 Respiratory pathogens: influenza A and B, respiratory syncytial virus†Nasopharyngeal±oropharyngeal swabLuminex respiratory panel
Paediatric viraemia and/or bacteraemia‡EDTA whole bloodPCR(Details to be determined)
  • *At sites where HIV prevalence is >1% in the general adult population.

  • †The Luminex respiratory panel also detects adenovirus, parainfluenza viruses 1–4, enterovirus, rhinovirus, B virus, coronaviruses (229E, OC43, HKu1 and NL63), metapneumovirus, bocavirus, Legionella pneumoniae, Chlamydia pneumoniae and Mycoplasma pneumoniae.

  • ‡To be performed on samples from children aged <5 years, from whom blood volumes will not be adequate for all serology tests listed.

  • EIA, enzyme immunoassay; EUCAST, European Committee of Antimicrobial Susceptibility Testing; IFA, immunofluorescence assay; MALDI-TOF MS, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry; mRDT, malaria rapid diagnostic test; qPCR, quantitative PCR.