Table 2.
Pathogen-based diagnostic testing for the Febrile Illness Evaluation in a Broad Range of Endemicities (FIEBRE)
| Infection or pathogen sought | Sample type | Diagnostic test | Notes |
| Pathogen-based diagnostic tests to be performed at or near the point of care | |||
| Malaria (Plasmodium species) | EDTA whole blood | Antigen-detecting lateral flow malaria rapid diagnostic test (mRDT) | Combination test detects histidine-rich protein 2 and Plasmodium lactate dehydrogenase |
| Thick and thin blood smear | Expert light microscopy for the presence versus the absence of asexual parasites, species and density | For all mRDT-positive samples and 10% of mRDT-negative samples | |
| HIV* | EDTA whole blood | Antibody-detecting rapid tests according to national guidelines | Confirmatory molecular testing according to national guidelines for infants who test antibody-positive |
| Bacteraemia and/or fungaemia | Whole blood | Aerobic culture, identification and antimicrobial susceptibility testing performed for isolated microorganisms | Single culture bottle; blood volume of ≤10 mL, weight-based volumes for small children |
| Mycobacteraemia* | Whole blood | Mycobacterial culture | For patients aged ≥15 years who are HIV-infected and/or admitted as inpatients |
| Mycobacterium tuberculosis | Urine | Urinary lipoarabinomannan rapid test | For patients who are HIV-infected and/or admitted as inpatients |
| Cryptococcus species | Serum | Antigen-detecting lateral flow rapid diagnostic test | For patients who are HIV-infected and/or admitted as inpatients |
| Nitrites and leucocyte esterase (evidence of urinary tract infection) | Urine | Urine dipstick | Urine culture performed on samples positive for nitrites and/or leucocyte esterase |
| Bacteriuria | Urine | Culture, identification and antimicrobial susceptibility testing performed for isolated microorganisms | For 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 smear | Expert light microscopy for the presence versus the absence of asexual parasites, species and density | Randomly 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 sites | Cryopreserved isolates | MALDI-TOF MS for identification and drug susceptibility testing to EUCAST standards | – |
| Mycobacteria isolated from blood at sites | Cryopreserved isolates | Identification 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 smear | Expert light microscopy | Random 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, Zika | Serum | Africa-specific or Asia-specific IgG ELISA and qPCR, microneutralisation for samples positive by ELISA | A 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) | Serum | Brucella IgM EIA, Brucella microagglutination test for samples positive by EIA | Convalescent sera screened for exposure using EIA; positives tested by IgM EIA and microagglutination on acute and convalescent sera |
| Leptospira species (leptospirosis) | Serum | Microagglutination test | – |
| Rickettsiae: Orientia species, Rickettsia (typhus group and spotted fever group), Coxiella burnetii | Serum and buffy coat | IgG and IgM IFA; qPCRfor samples positive by serological screen | Buffy coat is preferred sample for Orientia and rickettsial species detection, serum to be used for C. burnetii |
| Visceral leishmaniasis | Serum | Direct agglutination test | – |
| Histoplasma species (histoplasmosis) | Serum | Histoplasma EIA†† | – |
| Respiratory pathogens: influenza A and B, respiratory syncytial virus† | Nasopharyngeal±oropharyngeal swab | Luminex respiratory panel | – |
| Paediatric viraemia and/or bacteraemia‡ | EDTA whole blood | PCR | (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.