Hart C. Anthony, Shears Paul. Color Atlas of Medical Microbiology.pdf

DNA Viruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

Viruses with Single-Stranded DNA Genomes. . . . . . . . . . . . . 412

Parvoviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

Viruses with Double-Stranded DNA Genomes . . . . . . . . . . . 413

Papillomaviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413 Polyomaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415 Adenoviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416 Herpesviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418 Poxviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426

Hepadnaviruses: Hepatitis B Virus and

Hepatitis D Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429

RNA Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434

Viruses with Single-Stranded RNA Genomes,

Sense-Strand Orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434 Picornaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434

Astrovirus and Calicivirus; Hepatitis E. . . . . . . . . . . . . . . . 438

Astroviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439 Caliciviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439 Hepatitis E Virus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440 Togaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440 Flaviviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442 Coronaviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446 Retroviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 448

Human Immune Deficiency Virus (HIV) . . . . . . . . . . . . . . 451 Viruses with Double-Stranded RNA Genomes. . . . . . . . . . . . 455

Reoviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455

Viruses with Single-Stranded RNA Genomes, Antisense-Strand Orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457

Orthomyxoviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458 Bunyaviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460 Arenaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462 Paramyxoviruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464 Rhabdoviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467

Filoviruses (Marburg and Ebola Viruses) . . . . . . . . . . . . . 471

Subviral Pathogens: Viroids and Prions. . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Viroids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Prions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

Contents XXV

Echinococcus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565

Hymenolepis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575

Diphyllobothrium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575

Arachnida . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607

Ticks (Ixodida) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607

Mites. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 610

Insects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 612

Lice (Anoplura) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 612

Bugs (Heteroptera) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616

Mosquitoes and Flies (Diptera: Nematocera and

Brachycera) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616

Fleas (Siphonatera) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618

Appendix to Chapters 9–11. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621

Shipment of Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621

Stool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621

Blood. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622

XXVI Contents

Serum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Cerebrospinal Fluid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Bronchial Specimens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Urine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Cultivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Material for Polymerase Chain Reaction. . . . . . . . . . . . . . . . . . . . . . . . . . . 624 Tissue Specimens and Parasites. . . . . . . . . . . . . . . . . . . . . . . 624

Immunodiagnostic and Molecular Techniques . . . . . . . . . . . . . . . . . . . . . 624

2

11 General Aspects of Medical Microbiology

F. H. Kayser

&Infectious diseases are caused by subcellular infectious entities (prions, viruses), prokaryotic bacteria, eukaryotic fungi and protozoans, metazoan animals, such as parasitic worms (helminths), and some arthropods. Definitive proof that one of these factors is the cause of a given infection is demonstrated by fulfillment of the three Henle-Koch postulates. For technical rea-

sons, a number of infections cannot fulfill the postulates in their strictest sense as formulated by R. Koch, in these cases a modified form of the postulates is applied. &

The History of Infectious Diseases

The Past

Infectious diseases have been known for thousands of years, although accurate information on their etiology has only been available for about a century. In the medical teachings of Hippocrates, the cause of infections occurring frequently in a certain locality or during a certain period (epidemics) was sought in “changes” in the air according to the theory of miasmas. This concept, still reflected in terms such as “swamp fever” or “malaria,” was the predominant academic opinion until the end of the 19th century, despite the fact that the Dutch cloth merchant A. van Leeuwenhoek had seen and described bacteria as early as the 17th century, using a microscope he built himself with a single convex lens and a very short focal length. At the time, general acceptance of the notion of “spontaneous generation”—creation of life from dead organic material—stood in the way of implicating the bacteria found in the corpses of infection victims as the cause of the deadly diseases. It was not until Pasteur disproved the doctrine of spontaneous generation in the second half of the 19th century that a new way of thinking became possible. By the end of that century, microorganisms had been identified as the causal agents in many familiar diseases by applying the Henle-Koch postulates formulated by R. Koch in 1890.

The History of Infectious Diseases 3

The Henle–Koch Postulates

1

The postulates can be freely formulated as follows:

&The microorganism must be found under conditions corresponding to the pathological changes and clinical course of the disease in question.

&It must be possible to cause an identical (human) or similar (animal) disease with pure cultures of the pathogen.

&The pathogen must not occur within the framework of other diseases as an “accidental parasite.”

These postulates are still used today to confirm the cause of an infectious disease. However, the fact that these conditions are not met does not necessarily exclude a contribution to disease etiology by a pathogen found in context. In particular, many infections caused by subcellular entities do not fulfill the postulates in their classic form.

The Present

The frequency and deadliness of infectious diseases throughout thousands of years of human history have kept them at the focus of medical science. The development of effective preventive and therapeutic measures in recent decades has diminished, and sometimes eliminated entirely, the grim epidemics of smallpox, plague, spotted fever, diphtheria, and other such contagions. Today we have specific drug treatments for many infectious diseases. As a result of these developments, the attention of medical researchers was diverted to other fields: it seemed we had tamed the infectious diseases. Recent years have proved this assumption false. Previously unknown pathogens causing new diseases are being found and familiar organisms have demonstrated an ability to evolve new forms and reassert themselves. The origins of this reversal are many and complex: human behavior has changed, particularly in terms of mobility and nutrition. Further contributory factors were the introduction of invasive and aggressive medical therapies, neglect of established methods of infection control and, of course, the ability of pathogens to make full use of their specific genetic variability to adapt to changing conditions. The upshot is that physicians in particular, as well as other medical professionals and staff, urgently require a basic knowledge of the pathogens involved and the genesis of infectious diseases if they are to respond effectively to this dynamism in the field of infectiology. The aim of this textbook is to impart these essentials to them.

Table 1.1 provides an overview of the causes of human infectious diseases.

4 1 General Aspects of Medical Microbiology

Table 1.1 Human Pathogens

1

Pathogens

Subcellular Infectious Entities

& Prions (proteinaceous infectious particles). The evidence indicates that prions are protein molecules that cause degenerative central nervous system (CNS) diseases such as Creutzfeldt-Jakob disease, kuru, scrapie in sheep, and bovine spongiform encephalopathy (BSE) (general term: transmissible spongiform encephalopathies [TSE]).

Viruses. Ultramicroscopic, obligate intracellular parasites that:

—contain only one type of nucleic acid, either DNA or RNA,

—possess no enzymatic energy-producing system and no protein-synthe- sizing apparatus, and

—force infected host cells to synthesize virus particles.

Prokaryotic and Eukaryotic Microorganisms

According to a proposal by Woese that has been gaining general acceptance in recent years, the world of living things is classified in the three domains bacteria, archaea, and eucarya. In this system, each domain is subdivided into