Diagnostic tests

List of microbiological tests performed at the Croatian Institute of Public Health:







1.   Direct methods

a) Isolation and identification of pathogenic bacteria

  • enteric samples
  • respiratory samples
  • genital and urinary samples
  • aspirate, punctate, wounds etc.
  • pleural and other biopsy materials

If bacteria such as Listeria, Clostridium, Bordetella, Mycoplasma pneumoniae, Corynebacterium diphtheriae, Bacillus anthracis, Neisseria meningitidis,Vibrio cholerae, Legionella pneumophila and others are suspected, please specify on the request form.

b) Immunodiagnostic detection of antigents to pathogenic bacterial strains

  • Detection of Helicobacter pylori antigen in the stool

c)  PCR nucleic acid detection

  • Chlamydia trachomatis
  • Chlamydia pneumoniae
  • Mycoplasma pneumoniae
  • Legionella pneumophila
  • Neisseria meningitidis (A, B, C, Y, W135)
  • Neisseria gonorrhoeae
  • Ureaplasma spp.
  • Mycoplasma genitalium
  • Borrelia burgdorferi
  • Leptospira interrogans
  • Bordetella pertussis

d)  Diffusion antibiotic susceptibility testing

  • antibiogram

e)  Automated identification and susceptibility testing of bacteria and yeast

f)  Bacteriological analysis for hospital infection surveillance

  • haemodialysis water samples
  • dialysate samples
  • inanimante environment samples (surface and medical equipment swabs)
  • swabs from intensive care and surgical personnel (e.g. hand, laryngeal, nasal, nasophyringeal, axillary)

g)  Biological control of dry sterilization and/or autoclaving procedures

2.   Indirect methodsSEROLOGICAL TESTING for the presence of bacterial antigens in patients’ sera

  • Beta haemolytic streptococci:
    ASOT – Antistreptolysin O titre  (nephelometry)
    ADB – Anti-DNase B (ND)
  • Staphylococcus aureus – ASTA – Antistaphylolysin titre (latex-AG)
  • Bordetella pertussis (EIA)
  • Bordetella parapertussis  (EIA)
  • Borrelia burgdorferi (Lyme) (IFA, EIA, WB)
  • Francisella tularensis (tularaemia) (AG)
  • Legionella pneumophila (IFA)
  • Leptospira interrogans (AG-LY)
  • Listeria monocytogenes (IFA)
  • Syphilis, lues VDRL (RPR)
  • Treponema pallidum (TPHA, EIA)
  • salmonellosis (Widal agglutination)
  • brucellosis (Wright agglutination)
  • shigellosis (AG)
  • yersiniosis (AG)
  • Helicobacter pylori  (EIA IgA & IgG)
  • Mycoplasma pneumoniae (EIA IgM, IgG & IgA)
  • Chlamydophila pneumoniae (IFA IgA & IgG)
  • Chlamydophila (IFA IgA & IgG)
  • Chlamydia trachomatis (IFA IgA & IgG)
  • Coxiella burnetii (IFA IgM & IgG)
  • Rickettsia typhi (Murine typhus) (IFA IgM & IgG)
  • Rickettsia conorii (Mediterranean Spotted Fever) (IFA IgM & IgG)

EIA – enzyme immunoassay
AG – agglutination
AG-LY – agglutination and lysis
IFA – indirect imunofluorescence assay
WB – Western blott
TPHA – Treponema pallidum haemagglutination
RPR – rapid plasma reagin (corresponds to VDRL test)
IH – haemolysis inhibition
Latex-AG – latex agglutination

3. Mycobacteria testing (tuberculosis agents and non-tuberculous mycobacteria)

  • Direct microscopy for the presence of acid-fast bacilli
  • Cultivation on solid and liquid substrates
  • Identification of species within the Mycobacterium genus
  • Phenotypic and molecular detection of  M. tuberculosis resistance to anti-tuberculosis drugs
  • Real-time PCR (GeneXpert)
  • Quantiferon test
  • Molecular genotyping (MIRU-VNTR)


1.  Direct methods

a) Isolation of viruses from different clinical samples

  • Polioviruses, Enteroviruses, Echovirus, Coxsackievirus
  • Parechovirus
  • HSV (Herpes simplex virus) type 1/type 2
  • Influenza virus type A/type B
  • Mumps virus (Parotitis v.)
  • Measles virus (Morbilli v.)
  • Adenoviruses
  • Cytomegalovirus (CMV)

b) Direct testing for the presence of antigens in different clinical samples

  • stool – Noroviruses, Astrovirus, Rotavirus, Adenoviruses
  • respiratory tract and eye samples – Influenza virus A and B, Parainfluenza virus 1, 2 & 3, Adenoviruses, RSV, Human metapneumovirus
  • skin lesion swab – Varicella zoster virus (VZV)

c) Viral diagnostics in drinking and waste water

  • Polio viruses
  • Echo viruses
  • Coxackie viruses
  • Enteroviruses
  • Hepatitis A virus
  • Rotavirus
  • Noroviruses

d) PCR nucleic acid detection

  • Influenza virus type A
  • Influenza virus subtype A/H1, A/H3, A/H5, A/H7, A/H1pdm09
  • Influenza virus type B – Victoria-line
  • MERS, Coronavirus
  • Mumps virus (Parotitis v.)
  • Measles virus (Morbilli v. )
  • RSV type A/ type B
  • hMPV
  • Cytomegalovirus (CMV)
  • Enteroviruses (Polioviruses, ECHO viruses, Coxsackie virus)
  • Hepatitis A virus
  • Rubella virus
  • Tick-borne encephalitis virus (TBEV)
  • Dengue virus
  • West Nile virus (WNV)
  • Zika virus
  • Epstein-Barr virus (EBV)
  • Herpes virus type 1/ type 2 (HSV)
  • Noroviruses
  • HPV

2.   Indirect viral diagnostics – SEROLOGICAL TESTING for the presence of antibodies to viral antigens in patients’ sera

  • Tick-borne encephalitis virus (EIA IgM & IgG, IgG avidity)
  • Lymphocyte choriomeningitis virus (diagnostics being introduced)
  • Polio virus 1-3 (EIA IgG)
  • ECHO viruses (IFA IgM i IgG)
  • Coxsackie viruses (IFA IgM & IgG)
  • Mumps virus (Parotitis v.) (IFA IgM & IgG)
  • Herpes simplex virus 1, 2 (EIA IgM & IgG, WB IgM & IgG)
  • Adenoviruses (EIA IgM & IgG)
  • Influenzae A, B virus  (EIA IgM & IgG)
  • Parainfluenza virus (EIA IgM & IgG)
  • Respiratory syncytial virus (EIA IgM & IgG)
  • Morbilli virus (EIA IgM & IgG, IFA IgM & IgG)
  • Rubella virus  (EIA IgM & IgG, IgG aviditet)
  • Varicella zoster virus (EIA IgM, IgG & IgA, IgG avidity)
  • Cytomegalovirus (EIA IgM & IgG, IgG avidity)
  • Epstein-Barr virus (EIA IgM & IgG, IgG avidity, IFA EA, IFA EBNA)
  • Hantaviruses: Puumala, Dobrava, Hantaan, Saaremaa, Seoul (haemorrhagic fever with renal syndrome ) (IFA IgM & IgG)
  • West Nile virus (EIA IgM & IgG, IgG aviditet)
  • Dengue virus (EIA IgM & IgG)
  • Usutu virus (EIA IgG)
  • Pappataci or sand fly fever virus (Sicilian, Naples, Toscana) (IFA IgM & IgG)
  • Zika virus (EIA IgM & IgG)
  • Chikungunya virus (IFA IgM, IgG)
  • Arbovirus mosaic: dengue, Zika, chikungunya virus (IFA IgM, IgG)
  • HIV p24; anti HIV-1/2 (ELFA)
  • Hepatitis B virus: HBsAg, anti-HBs, anti-HBc, anti-HBc IgM, HBeAg, anti-HBe (ELFA)
  • Hepatitis C virus: anti-HCV (ELFA)
  • Hepatitis A virus: anti-HAV, anti-HAV IgM (ELFA)


EIA – enzyme immunoassay
IFA – indirect imunofluorescence assay
WB – Western blott
ELFA – enzyme-linked fluorescence assay


1.  Direct methods

a) Identification of parasitic elements from different clinical samples

  • Protozoa cysts and helminth eggs (native preparation, concentration methods, coproculture) – stool
  • Coccidia (Cryptosporidium, Cyclospora, Isospora) staining, autofluorescence – stool
  • perianal tape test for Enterobius
  • female genital samples, semen, urine, male urethral swab for Trichomonas vaginalis (native preparation, cultivation, PCR)
  • biopsy material for tissue parasites (native, staining, histological preparation)
  • detection of parasites in body fluids (native, staining, histological preparation, miracidia test)
  • thick and thin blood smear for Plasmodium falciparum, vivax, ovale, malariae, knowlesi, Babesia, Trypanosoma brucei, Trypanosoma cruzi, microfilariae
  • protozoa cultivation (Leishmania, Trihomonas, Entamoeba histolytica, free-living amoebae – Acanthamoeba spp, Naegleria fowleri, Balamuthia mandrilaris)
  • macro- and microscopic helminth and arthropod identification

b) Detection of parasite antigens

  • Entamoeba histolytica in stool (EIA)
  • Cryptosporidium sp. in stool (EIA)
  • Giardia lamblia (EIA)
  • Plasmodium falciparum (IC)

c) PCR nucleic acid detection

  • Trichomonas vaginalis
  • Toxoplasma gondii
  • Leishmania sp.
  • Acanthamoeba

2.   Indirect methods – SEROLOGICAL TESTING for the presence of antibodies to parasitic antigens in patients’ sera

  • toxoplasmosis (ELFA IgM, IgG, EIA IgA; ELFA AV IgG, ISAGA IgM, IgA IGg, WB comparative IgG-IgM)
  • echinococcosis (EIA, WB)
  • cysticercosis – Taenia solium (EIA, WB)
  • leishmaniasis (IFA, EIA, WB)
  • malaria (IFA)
  • toxocarosis (EIA, WB)
  • trichinellosis (EIA, WB)
  • amebiasis (IFA, EIA)
  • strongyloidiasis (EIA)
  • ascaridiasis (EIA)
  • fasciolosis (EIA; WB)
  • schistosomiasis (EIA)
  • American trypanosomiasis (EIA)

IFA – indirect imunofluorescence assay
IC – immunochromatographic assay
EIA – enzyme immunoassay
ELFA – enzyme-linked fluorescence assay
ISAGA – immunosorbent agglutination assay
AV IgG – IgG avidity assay (differentiation between recent and past infection)
WB – Western blott


1.  Direct methods

  • Identification of Cryptococcus neoformans capsular antigen in body fluids using latex agglutination (LA) test
  • Isolation and identification of fungi (yeast and moulds) from different clinical samples by cultivation in nutrient media and determination of biochemical properties
  • Yeast and mould antifungal susceptibility testing by diffusion method (E-test)
  • Yeast antifungal susceptibility testing by dilution method
  • Identification of strains (yeast and moulds) and determination of susceptibility test for isolates from other microbiology laboratories
  • Pneumocystis jiroveci PCR diagnostics
  • Dermatophyte diagnostics by direct microscoping and cultivation in nutrient media
  • Fungal diagnostics in inanimante environment samples

2.   Indirect methods – SEROLOGICAL TESTING for the presence of antibodies to fungal antigen in patients’ sera

  • Candida serology (IHA and EIA)
  • Systemic aspergillosis serology (EIA)
  • Systemic cryptococcosis serology (EIA)

IHA – indirect haemagglutination
EIA – enzyme immunoassay
LA – latex agglutination