Table 2.

List of diagnostic methods and sample selection for the most important notifiable bacterial diseases of poultry

Methods of diagnosis for bacterial-origin poultry and avian diseases
Infectious agent	Samples of choice	Serological techniques – Immune status	Etiological diagnosis – Identification of the agent
Fowl typhoid and pullorum disease: Salmonella	•Aseptically taken samples of tissues (spleen and liver), intestinal (cecal tonsil) or cloacal content, eggs, embryos, oviduct, fecal droppings and cloacal swabs, and hatcher debris	•Rapid whole blood plate or serum agglutination test	•Culture (MacConkey agar, xylose lysine, brilliant green agar, Rappaport–Vassiliadis soya, etc.) and biochemical test (API system for Enterobacteriaceae) •PCR-RFLP
Fowl cholera: Pasteurella	•Bone marrow, lung, liver, spleen, gonads and heart blood, and caseous exudates	•Rarely used for diagnosis of Fowl cholera	•Culture (Blood agar, trypticase-soy agar, and dextrose starch agar) and biochemical test •Somatic typing procedure using gel diffusion precipitin test •REA
Chlamydiosis	•Live birds: pharyngeal and nasal swabs, intestinal excrements, and conjunctival scraping •Dead birds: Inflammatory or fibrinous exudates (peritoneal or in organs); ocular and nasal exudates; impression smear of the liver; whole blood; and tissue samples of the kidney, lung, pericardium, spleen, liver, and colon contents or excrements	•ELISA, AGID •CF test, modified direct CF test, latex agglutination, and elementary body agglutination	•Isolation in embryonated chicken eggs or cell culture •Cytochemical staining of smears or immunohistochesmistry •Conventional and real-time PCR, restriction length polymorphism, DNA microarray, and sequencing
Mycoplasma	•Live birds: choanal cleft, oropharynx, eyes cloaca, and phallus swabs •Dead birds: nasal cavity, infraorbital sinus, trachea, air sacs, esophagus, joint cavities, and material of egg yolk or embryos	•RSA test •ELISA •HI test	•Culture in specific media •Basic biochemical test (i.e., fermentation of glucose and failure to hydrolyze arginine) •Immunofluorescent antibodies and immunoperoxidase test
Tuberculosis	•Liver or spleen tissue samples and bone marrow	•Tuberculin test •Blood stained-antigen agglutination test	•Detection of acid-fast bacilli in smears or tissue sections from affected organs •Culture (Lowenstein–Jensen, Herrol'd medium and other media) •Typing methods: ELISA and HPLC •PCR, multiplex-PCR, and PCR-RFLP

Abbreviations: AGID, agar gel immunodiffusion; API, analytical profile index; CF, complement fixation; ELISA, enzyme-linked immunosorbent assay; HI, hemagglutination inhibition; HPLC, high-performance liquid chromatography; PCR, polymerase chain reaction; PCR-RFLP, PCR-restriction fragment length polymorphism; REA, restriction endonuclease analysis; and RSA, rapid serum agglutination.

Source: OIE, 2013a. Manual of diagnostic tests and vaccines for terrestrial animals: Avian influenza. In: Terrestrial Manual. International Standard Setting, seventh ed. World Organization for Animal Health, pp. 436–454 (Chapter 2.3.4) and OIE, 2013b. Chapter 2.3.4. Avian influenza. In: I. S. S. T. Manual (Ed.), World Organisation for Animal Health. Paris, France: World Organisation for Animal Health, Section 2.3 (Chapters: 2.3.1., 2.3.2., 2.3.3., 2.3.4., 2.3.5., 2.3.6., 2.3.9., 2.3.10., 2.3.11., 2.3.12., 2.3.13., 2.3.14).