Table 2.

Common types of clinical specimens and their application.

Type of infection	Specimen type	Examples of pathogens	Main purpose
Multi-drug-resistant bacteria	Sputum, stool, anal swab, nasal swab	Carbapenem resistance gene (CRE), Methicillin-resistant Staphylococcus aureus (MRSA)	Multi-drug-resistant bacteria control
Gastrointestinal tract infection	Stool, anal swab	Clostridium difficile	Detection of Clostridium difficile infection
Respiratory tract infection	Throat swab	Group A Streptococcus	Detection and identification of the aetiology of pharyngitis
	Nasopharyngeal swab	Acute respiratory viruses (influenza A virus, influenza B virus respiratory syncytial virus, SARS-CoV-2)	Used for the diagnosis of acute respiratory infections, guiding treatment, and assisting infection control
	Sputum/alveolar lavage fluid/tissue	Mycobacterium tuberculosis and rifampicin resistance Viruses, fungi, atypical pathogens	Screening and diagnosis of lower respiratory tract infections, guiding medication
Genitourinary tract infection	Urine, pus, cervical specimen, swab	Chlamydia trachomatis, Mycoplasma, Neisseria gonorrhoeae, HPV, GBS*	Screening and diagnosis of sexually transmitted diseases
Blood-borne infection	Blood	HIV, HBV, HCV*	Surgery/blood transfusion/haemodialysis/endoscopy preparation
Central nervous system infection	Cerebrospinal fluid	EV71, Japanese encephalitis virus, cryptococci, Mycobacterium tuberculosis	Diagnosis of central nervous system infection

*GBS, group B Streptococcus; HBV, hepatitis B virus; HCV, hepatitis C virus; HIV, human immunodeficiency virus; HPV, human papilloma virus.