Molecular Microbiology

Diagnostic Principles and Practice

David H. Persing, Fred C. Tenover, Randall T. Hayden, Margareta Ieven, Melissa B. Miller, Frederick S. Nolte, Yi-Wei Tang, Alex van Belkum, David H. Persing, Fred C. Tenover, Randall T. Hayden, Margareta Ieven, Melissa B. Miller, Frederick S. Nolte, Yi-Wei Tang, Alex van Belkum

• Publisher: ASM Press
• Year: 2016
• Print ISBN: 9781555819088
• eBook ISBN: 9781683673286
• Edition: 3
• Topic: Biological Sciences
• Subtopic: Microbiology
• Index: Biological Sciences

Presenting the latest molecular diagnostic techniques in one comprehensive volume

The molecular diagnostics landscape has changed dramatically since the last edition of Molecular Microbiology: Diagnostic Principles and Practice in 2011. With the spread of molecular testing and the development of new technologies and their opportunities, laboratory professionals and physicians more than ever need a resource to help them navigate this rapidly evolving field.

Editors David Persing and Fred Tenover have brought together a team of experienced researchers and diagnosticians to update this third edition comprehensively, to present the latest developments in molecular diagnostics in the support of clinical care and of basic and clinical research, including next-generation sequencing and whole-genome analysis. These updates are provided in an easy-to-read format and supported by a broad range of practical advice, such as determining the appropriate type and quantity of a specimen, releasing and concentrating the targets, and eliminating inhibitors.

Molecular Microbiology: Diagnostic Principles and Practice

• Presents the latest basic scientific theory underlying molecular diagnostics
• Offers tested and proven applications of molecular diagnostics for the diagnosis of infectious diseases, including point-of-care testing
• Illustrates and summarizes key concepts and techniques with detailed figures and tables
• Discusses emerging technologies, including the use of molecular typing methods for real-time tracking of infectious outbreaks and antibiotic resistance
• Advises on the latest quality control and quality assurance measures
• Explores the increasing opportunities and capabilities of information technology

Molecular Microbiology: Diagnostic Principles and Practice is a textbook for molecular diagnostics courses that can also be used by anyone involved with diagnostic test selection and interpretation. It is also a useful reference for laboratories and as a continuing education resource for physicians.

If you are looking for online access to the latest clinical microbiology content, please visit www.wiley.com/learn/clinmicronow.

section V

SYNDROMIC DIAGNOSTICS

24

Molecular Approaches to the Diagnosis of Meningitis and Encephalitis

KAREN C. BLOCH AND YI-WEI TANG

Karen C. Bloch, Departments of Medicine and Health Policy, Vanderbilt University School of Medicine, Nashville, TN 37232. Yi-Wei Tang, Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan-Kettering Cancer Center and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10065.

INTRODUCTION AND GENERAL DISCUSSION

Meningitis and encephalitis represent central nervous system (CNS) infections where rapid and accurate identification of an infectious agent is essential for management. CNS infections present a challenge for both the microbiologist and the clinician due to the vast number of pathogens associated with these syndromes (1, 2). Molecular diagnostic techniques such as PCR have replaced slower and less sensitive tests for a number of bacterial and viral causes of CNS infection (3). This chapter reviews various diagnostic tests available for CNS infections and provides a detailed discussion of specific molecular approaches to the most common organisms causing meningitis and encephalitis in the United States.

Pathophysiology of CNS Infections

The CNS has unique anatomic and immunologic characteristics that distinguish infection at this site from those involving other organ systems. The brain and spinal cord are contained within the bony confines of the calvarium and vertebral column. Cerebrospinal fluid (CSF) is produced in the choroid plexus of the ventricles and flows into the subarachnoid space at the cisterna magna and around the cerebral hemisphere, where it is reabsorbed by the arachnoid villi. CSF envelops the brain and spinal cord, providing cushioning and buoyancy for neural tissue. It carries essential metabolites into the neural tissue and cleanses the tissues of waste as it circulates around the brain, ventricles, and spinal cord. The blood-brain barrier (BBB) serves to limit the entry of microorganisms and inflammatory cells into the CNS. The absence of mediators of innate immunity in the CSF may contribute to the rapid progression and morbidity of CNS infections (4, 5). In addition, because of this anatomic barrier, antimicrobials used to treat CNS infections must have pharmacologic properties that allow them to penetrate the BBB, and maximal doses are usually required for bactericidal activity.

Meningitis

Meningitis involves infection localized to the subarachnoid space, sparing the brain parenchyma. While neural tissue is not directly infected, secondary damage may occur as a result of the host inflammatory response. Leukocyte migration into the subarachnoid space can result in occlusion of cortical blood vessels and damage to nerve roots that traverse the subarachnoid space. Clinically, this manifests as cranial or spinal nerve dysfunction and hydrocephalus. Activation of white blood cells leads to an inflammatory cascade, with release of cytokines, oxidants, and proteolytic enzymes. At the cellular level, this chain of events results in disruption of the BBB and impaired cerebrovascular autoregulation (6). Increased intracranial pressure may lead to transtentorial herniation or tissue hypoxia due to decreased tissue perfusion.

Encephalitis

Encephalitis is defined by the presence of an inflammatory process in the brain, associated with clinical evidence of neurologic dysfunction (7). Encephalitis can present with purely parenchymal findings but more commonly is associated with meningeal inflammation, representing an overlap syndrome termed meningoencephalitis. Additionally, encephalitis can coexist with myelitis, inflammation of the spinal cord, to cause encephalomyelitis. These three syndromes are often grouped together due to the significant overlap in the epidemiology, microbiology, and approach to management.

Most infectious agents that cause encephalitis gain access to the CNS through hematogenous spread. The initial site of entry and replication varies depending on the organism and may include the respiratory tract (e.g., measles virus), gastrointestinal tract (e.g., enteroviruses), or skin (e.g., arboviruses). Viremia follows localized infection, ultimately leading to invasion and replication with the CNS.

Hematogenously spread CNS infections, such as arboviruses, generally cause diffuse brain involvement, with global impairment in neurologic function. Infections introduced through other routes typically involve specific areas of the brain. For instance, following the bite of an infected animal, rabies virus is inoculated subcutaneously, with retrograde progression along peripheral nerves into the brain stem (8). In contrast, the free-living amoeba Naeglaria fowleri enters the host transnasally, passing through the cribiform plate and invading the frontal lobes of the brain (9). The pathogenesis of herpes simplex encephalitis (HSE) is believed to occur following reactivation of the virus in the trigeminal ganglion, with spread to the frontal and temporal lobes via the tentorial nerves (10).

Classification of CNS Infections

CNS infections are typically classified based on the anatomic site of infection. Infection of the meninges, brain, and spinal cord results in the syndromes of meningitis, encephalitis, and myelitis, respectively. Focal CNS infections include abscess, subdural empyema, or subarachnoid empyema. Infection may be limited to a single anatomic compartment or may involve multiple sites (e.g., meningoencephalitis, encephalomyelitis). Acute meningitis is characterized by the onset of the triad of fever, headache, and neck stiffness over a period of hours to days (11). The hallmark of encephalitis is alteration in mental status, ranging from lethargy to coma. Myelitis is characterized by inflammation of the spinal cord with symptoms including fever, headache, and paraparesis or paralysis.

Meningitis and encephalitis are the two most common CNS infections and are covered in detail in this chapter. Differentiation of these two syndromes is important, because both the pathophysiology and microbiology of meningitis and encephalitis are distinct....

Table of contents

• Cover Page
• Title Page
• Copyright Page
• Contents
• Contributors
• Preface
• Section I: Novel and Emerging Technologies
• Section II: Metagenomics: Implications for Diagnostics
• Section III: Health Care-Associated Infections
• Section IV: Molecular Diagnostics and Public Health
• Section V: Syndromic Diagnostics
• Section VI: Virology
• Section VII: Fungi and Protozoa
• Section VIII: Point-of-Care/Near-Care Diagnostics
• Section IX: The Host and Host Response
• Section X: Information Technology
• Section XI: Quality Assurance
• Section XII: The Business of Diagnostics
• Index