Molecular Diagnostics of Infectious Diseases

Harald H. Kessler

• Publisher: De Gruyter
• Year: 2014
• eBook ISBN: 9783110373479
• Edition: 3
• Topic: Medicine
• Subtopic: Biochemistry in Medicine

The prevalence of infectious diseases is worldwide increasing. Therefore, detection methods for infectious pathogens change quickly. In the 3rd edition of Kessler´s Molecular Diagnostics of Infectious Diseases laboratory professionalists get valueable information about the current diagnostic methods, tipps and tricks in terms of sample processing, quality control, and interpretation of the results. For clinicians the book is a valuable aid for decision-making in ordering appropriate tests as well as in assuring the necessary quality of the sample material.

1 Choice of adequate sample material

Holger F. Rabenau, Reinhard B. Raggam, Margit Hübner and Eva Leitner

Nucleic acid amplification testing (NAT) has gained major impact on the detection of pathogens. Today, NAT is widely used in the routine diagnostic laboratory. It is employed in special situations including the very early stage of infection before production of antibodies and in patients lacking antibody production due to immunosuppression. Furthermore, NAT is the method of choice to detect/exclude vertical transmission and to monitor therapy.

Reliable molecular diagnostics strongly depends on preanalytical issues including the choice of adequate sample material, optimal sampling time regarding the course of disease, and both time and conditions of the sample transport to the laboratory.

This chapter focuses on the choice of adequate sample materials for molecular diagnostics of viruses, bacteria, fungi, and protozoa. Pathogens with epidemiological and clinical significance for which molecular diagnostics plays an important role are discussed in alphabetical order.

1.1 Viruses

Adenoviruses (Family: Adenoviridae; approx. 50 human serotypes, subgenera A–F) Epidemiology: worldwide distribution.

Transmission: droplets and smear infection; entrance gates are eyes and the oropharynx.

Incubation period: 5–12 days.

Clinical presentation: adenovirus infections are often asymptomatic or cause respiratory tract infections, gastroenteritis, and epidemic keratoconjunctivitis.

Complications: meningoencephalitis in children, disseminated, sepsis-like adenoviral infection with multiple organ manifestations in immunosuppressed patients.

Indication and choice of the adequate sample material for NAT:

Clinical presentation	Sample material
Epidemic keratoconjunctivitis	Conjunctival swab
Upper respiratory tract infection	Nasopharyngeal swab or aspirate, throat washing, induced sputum
Pneumonia	Bronchoalveolar lavage (BAL), EDTA whole blood
Hemorrhagic cystitis	Urine
Encephalitis	Cerebrospinal fluid (CSF)
Gastroenteritis	Stool
Pre-emptive monitoring/suspected adenovirus infection under immunosuppression	EDTA whole blood, nasopharyngeal swab or aspirate, throat washing, urine

Astrovirus (Family: Astroviridae)

Epidemiology: occasional outbreaks, e.g. in nursing homes or nosocomial outbreaks in hospitals.

Transmission: smear infections or through contaminated food and water.

Incubation period: 1–3 days.

Clinical presentation: gastroenteritis with fever, vomiting and abdominal pain.

Indication and choice of the adequate sample material for NAT:

Clinical presentation	Sample material
Gastroenteritis	Stool

Bocavirus (BoV) (Family: Parvoviridae; 4 species: BoV1–BoV4)

Epidemiology: worldwide distribution, in 2–19% of patients with upper or lower respiratory tract disease predominantly during winter and spring, very common during early childhood, co-infections with other respiratory viruses frequently observed, BoV2 through BoV4 mainly in stool (enteric species), associated with gastroenteritis, co-infections with other gastrointestinal viruses in up to 100% of stool specimens.

Transmission: Transmission routes unknown; however, most likely transmitted by inhalation or contact with infectious sputum, feces, or urine.

Incubation period: Unknown.

Clinical presentations: BoV1: Respiratory tract infection with cough and wheeze, rhinorrhea, tachypnea, and fever. BoV2 through BoV4: Gastroenteritis.

Complications: Rash or exanthema, thrombopenia, pneumonia, sepsis (rarely).

Indication and choice of the adequate sample material for NAT:

Clinical presentation	Sample material
Upper respiratory tract infection	Nasopharyngeal swab or aspirate, throat washing
Pneumonia	BAL
Gastroenteritis	Stool

Note: BoV may persist in the respiratory or gastrointestinal tract as a bystander without symptoms resulting in frequent detection of BoV.

Coronaviruses (Family: Coronaviridae; 4 genera: alpha including the human CoVs229E and NL229E, beta including the human CoVsOC43, HKU1, MERS-CoV, and SARS-CoV, gamma including only avian pathogens, and the provisional delta genus)

Epidemiology: worldwide distribution depending on genus, high prevalence already in childhood.

Transmission: droplets and smear infection.

Incubation period: 2–5 days (SARS 2–20 days, MERS 5-12 days).

Clinical presentation: Respiratory tract infections. MERS/SARS disease with fever, cough, shortness of breath, pneumonia, and bronchiolitis; CoV-NL229E occurs especially in children with disorders of the upper respiratory tract, pneumonia, and bronchiolitis.

Indication and choice of the adequate sample material for NAT:

Clinical presentation	Sample material
Upper respiratory tract infection	Nasopharyngeal swab or aspirate, throat washing, induced sputum
Pneumonia, bronchiolitis	BAL
Suspected MERS/SARS infection	Nasopharyngeal swab or aspirate, throat washing, induced sputum, BAL

Cytomegalovirus (CMV) (Family: Herpesviridae)

Epidemiology: worldwide distribution, seroprevalence 50–100%.

Transmission: oro-oral contact (kissing) through saliva, and sexually through genital secretions, rarely droplets or smear infection; pre- and perinatal; possibly iat...

Table of contents

• Also of Interest
• Title Page
• Copyright Page
• Preface to the Third Edition
• Table of Contents
• Authors Index
• Contributors Index
• 1 Choice of adequate sample material
• 2 Stability of the specimen during preanalytics
• 3 Quality assurance and quality control
• 4 Extraction of nucleic acids
• 5 Amplification and detection methods
• 6 Interpreting and reporting molecular diagnostic tests
• 7 Human immunodeficiency virus
• 8 Hepatitis viruses
• 9 Pathogens relevant in transplantation medicine
• 10 Pathogens in lower respiratory tract infections
• 11 Molecular diagnosis of gastrointestinal pathogens
• 12 Pathogens relevant in the central nervous system
• 13 Pathogens relevant in sexually transmitted infections
• Index