Jawetz Melnick & Adelbergs Medical Microbiology 28th

Edition

Visit the link below to download the full version of this book:

https://medidownload.com/product/jawetz-melnick-adelbergs-medical-microbiology-2
8th-edition/

Click Download Now

 Preface

As all the prior editions of this textbook before, the twenty- Chapter 48 was specifically updated to reflect clinically impor-
eighth edition of Jawetz, Melnick, & Adelberg’s Medical tant and currently emerging infectious disease cases.
Microbiology remains true to the goals of the first edition New to this edition are Peter Hotez, MD, PhD, Rojelio
published in 1954, which is to “to provide a brief, accurate Mejia, MD, and Stefan Riedel, MD, PhD, D(ABMM).
and up-to-date presentation of those aspects of medical Dr. Hotez is the Dean of the National School of Tropical Medi-
microbiology that are of particular significance to the fields cine at Baylor College of Medicine in Houston, TX, and is a
of clinical infections and chemotherapy.” Professor of Pediatrics, Molecular Virology and Microbiology;
For the twenty-seventh edition, under the authorship of he brings extensive expertise in parasitology. Dr. Mejia is an
Dr. Karen Carroll, all chapters had been extensively revised, Assistant Professor in the Department of Pediatrics, Section
reflecting the tremendous expansion of medical knowledge of Tropical Medicine, at the National School of Tropical Medi-
afforded by molecular mechanisms and diagnostics, advances cine, Baylor College of Medicine in Houston, TX. Dr. Riedel
in our understanding of microbial pathogenesis, and the dis- is the Associate Medical Director of the Clinical Microbiol-
covery of novel pathogens. While Dr. Carroll decided to step ogy Laboratories at Beth Israel Deaconess Medical Center in
down as an author and contributor for this new edition, the Boston, MA, and holds the academic rank of Associate Pro-
remaining authors would like to express their gratitude for her fessor of Pathology at Harvard Medical School. Following
leadership and contributions to the previous, greatly expanded Dr. Carroll’s departure as an author and contributor to this
edition. For the 28th edition, Chapter 47, “Principles of Diag- textbook, Dr. Riedel assumed the role as Editor-in-Chief for
nostic Medical Microbiology,” and Chapter 48, “Cases and this revised, 28th edition of the textbook.
Clinical Correlations,” were again updated to reflect the con- The authors hope that the changes to this current edition
tinued expansion in laboratory diagnostics as well as new will continue to be helpful to the student of microbiology and
antimicrobial therapies in the treatment of infectious diseases. infectious diseases.

xi

Riedel-FM_pi-xii.indd 11 05/04/19 6:25 PM

 This page intentionally left blank

Riedel-FM_pi-xii.indd 12 05/04/19 6:25 PM

 SECTION I FUNDAMENTALS OF MICROBIOLOGY

1
C H A P T E R

The Science of Microbiology

INTRODUCTION it biochemical property or genetic mechanism, analysis of

microorganisms takes us to the limits of biologic understand-
Microbiology is the study of microorganisms, a large and diverse ing. Thus, the need for originality—one test of the merit of
group of microscopic organisms that exist as single cells or cell a scientific hypothesis—can be fully met in microbiology. A
clusters; it also includes viruses, which are microscopic but not useful hypothesis should provide a basis for generalization,
cellular. Microorganisms have a tremendous impact on all life and and microbial diversity provides an arena in which this chal-
the physical and chemical makeup of our planet. They are respon- lenge is ever present.
sible for cycling the chemical elements essential for life, including Prediction, the practical outgrowth of science, is a prod-
carbon, nitrogen, sulfur, hydrogen, and oxygen; more photosyn- uct created by a blend of technique and theory. Biochemistry,
thesis is carried out by microorganisms than by green plants. molecular biology, and genetics provide the tools required
Furthermore, there are 100 million times as many bacteria in the for analysis of microorganisms. Microbiology, in turn,
oceans (13 × 1028) as there are stars in the known universe. The extends the horizons of these scientific disciplines. A biolo-
rate of viral infections in the oceans is about 1 × 1023 infections per gist might describe such an exchange as mutualism, that
second, and these infections remove 20–40% of all bacterial cells is, one that benefits all contributing parties. Lichens are an
each day. It has been estimated that 5 × 1030 microbial cells exist example of microbial mutualism. Lichens consist of a fungus
on earth; excluding cellulose, these cells constitute about 90% of and phototropic partner, either an alga (a eukaryote) or a
the biomass of the entire biosphere. Humans also have an intimate cyanobacterium (a prokaryote) (Figure 1-1). The phototro-
relationship with microorganisms; 50–60% of the cells in our bod- pic component is the primary producer, and the fungus pro-
ies are microbes (see Chapter 10). The bacteria present in the aver- vides the phototroph with an anchor and protection from the
age human gut weigh about 1 kg, and a human adult will excrete elements. In biology, mutualism is called symbiosis, a con-
his or her own weight in fecal bacteria each year. The number of tinuing association of different organisms. If the exchange
genes contained within this gut flora outnumber that contained operates primarily to the benefit of one party, the association
within our genome by 150-fold; even in our own genome, 8% of is described as parasitism, a relationship in which a host pro-
the DNA is derived from remnants of viral genomes. vides the primary benefit to the parasite. Isolation and char-
acterization of a parasite—such as a pathogenic bacterium or
virus—often require effective mimicry in the laboratory of
BIOLOGIC PRINCIPLES ILLUSTRATED the growth environment provided by host cells. This demand
BY MICROBIOLOGY sometimes represents a major challenge to investigators.
The terms mutualism, symbiosis, and parasitism relate to
Nowhere is biologic diversity demonstrated more dramati- the science of ecology, and the principles of environmental
cally than by microorganisms, cells, or viruses that are not biology are implicit in microbiology. Microorganisms are the
directly visible to the unaided eye. In form and function, be products of evolution, the biologic consequence of natural

Riedel_CH01_p001-p010.indd 1 05/04/19 8:37 AM

 2   SECTION I   Fundamentals of Microbiology

Alga

Fungus

Fungal Cortex
hyphae

Alga
layer

Cortex

FIGURE 1-1 Diagram of a lichen, consisting of cells of a phototroph, either an alga or a cyanobacterium, entwined within the hyphae of
the fungal partner. (Reproduced with permission from Nester EW, Anderson DG, Roberts CE, et al: Microbiology: A Human Perspective, 6th ed.
McGraw-Hill, 2009, p. 293. © McGraw-Hill Education.)

selection operating on a vast array of genetically diverse plant and animal hosts as well as protists, fungi, and bacteria.
organisms. It is useful to keep the complexity of natural his- However, most viruses are restricted to infecting specific
tory in mind before generalizing about microorganisms, the types of cells of only one host species, a property known as
most heterogeneous subset of all living creatures. “tropism”. Recently, viruses called virophages have been
A major biologic division separates the eukaryotes, discovered that infect other viruses. Host–virus interactions
organisms containing a membrane-bound nucleus from pro- tend to be highly specific, and the biologic range of viruses
karyotes, organisms in which DNA is not physically sepa- mirrors the diversity of potential host cells. Further diversity
rated from the cytoplasm. As described in this chapter and in of viruses is exhibited by their broad array of strategies for
Chapter 2, further major distinctions can be made between replication and survival.
eukaryotes and prokaryotes. Eukaryotes, for example, are Viral particles are generally small (eg, adenovirus has a
distinguished by their relatively large size and by the pres- diameter of 90 nm) and consist of a nucleic acid molecule,
ence of specialized membrane-bound organelles such as either DNA or RNA, enclosed in a protein coat, or capsid (some-
mitochondria. times itself surrounded by an envelope of lipids, proteins,
As described more fully later in this chapter, eukary- and carbohydrates). Proteins—frequently glycoproteins—
otic microorganisms—or, phylogenetically speaking, the comprising the capsid and/or making up part of the lipid
Eukarya—are unified by their distinct cell structure and phy- envelope (e.g., HIV gp120) determine the specificity of inter-
logenetic history. Among the groups of eukaryotic microor- action of a virus with its host cell. The capsid protects the
ganisms are the algae, the protozoa, the fungi, and the slime nucleic acid cargo. The surface proteins, whether they are
molds. A class of microorganisms that share characteristics externally exposed on the capsid or associated with the enve-
common to both prokaryotes and eukaryotes are the archae- lope facilitates attachment and penetration of the host cell
bacteria and are described in Chapter 3. by the virus. Once inside the cell, viral nucleic acid redirects
the host’s enzymatic machinery to functions associated with
replication and assembly of the virus. In some cases, genetic
VIRUSES information from the virus can be incorporated as DNA into
a host chromosome (a provirus). In other instances, the viral
The unique properties of viruses set them apart from liv- genetic information can serve as a basis for cellular manufac-
ing creatures. Viruses lack many of the attributes of cells, ture and release of copies of the virus. This process calls for
including the ability to self-replicate. Only when it infects a replication of the viral nucleic acid and production of spe-
cell does a virus acquire the key attribute of a living system— cific viral proteins. Maturation consists of assembling newly
reproduction. Viruses are known to infect a wide variety of synthesized nucleic acid and protein subunits into mature

Riedel_CH01_p001-p010.indd 2 05/04/19 8:37 AM

 CHAPTER 1 The Science of Microbiology   3

viral particles, which are then liberated into the extracellu-

lar environment. Some very small viruses require the assis-
tance of another virus in the host cell for their replication.
The delta agent, also known as hepatitis D virus (HDV), has
a RNA genome that is too small to code for even a single
capsid protein (the only HDV-encoded protein is delta anti-
gen) and needs help from hepatitis B virus for packaging and
transmission.
Some viruses are large and complex. For example, Mimi-
virus, a DNA virus infecting Acanthamoeba, a free-living soil
ameba, has a diameter of 400–500 nm and a genome that
encodes 979 proteins, including the first four aminoacyl tRNA
synthetases ever found outside of cellular organisms. This
virus also encodes enzymes for polysaccharide biosynthesis,
a process typically performed by the infected cell. An even
larger marine virus has recently been discovered (Megavirus);
its genome (1,259,197-bp) encodes 1120 putative proteins and
is larger than that of some bacteria (see Table 7-1). Because of
their large size, these viruses resemble bacteria when observed
in stained preparations by light microscopy; however, they do
not undergo cell division or contain ribosomes. 50 µm

Several transmissible plant diseases are caused by FIGURE 1-2 Prion. Prions isolated from the brain of a scrapie-
viroids—small, single-stranded, covalently closed circu- infected hamster. This neurodegenerative disease is caused by a
lar RNA molecules existing as highly base-paired rod-like prion. (Reproduced with permission from Stanley B. Prusiner.)
structures. They range in size from 246 to 375 nucleotides in
length. The extracellular form of the viroid is naked RNA—
there is no capsid of any kind. The RNA molecule contains protein that prions are made of (PrP) is found through-
no protein-encoding genes, and the viroid is therefore totally out the body, even in healthy people and in animals, and is
dependent on host functions for its replication. Viroid RNA encoded by the host’s chromosomal DNA. The normal form
is replicated by the DNA-dependent RNA polymerase of the of the prion protein is called PrPc. PrPc is a sialoglycoprotein
plant host; preemption of this enzyme may contribute to with a molecular mass of 35,000–36,000 Da and a mainly
viroid pathogenicity. α-helical secondary structure that is sensitive to proteases
The RNAs of viroids have been shown to contain inverted and soluble in detergent. Several topological forms exist:
repeated base sequences (also known as insertion sequences) one cell surface form anchored by a glycolipid, and two
at their 3′ and 5′ ends, a characteristic of transposable ele- transmembrane forms. The disease scrapie manifests itself
ments (see Chapter 7) and retroviruses. Thus, it is likely that when a conformational change occurs in the prion protein,
they have evolved from transposable elements or retroviruses changing it from its normal or cellular form PrPc to the
by the deletion of internal sequences. infectious disease-causing isoform, PrPSc (Figure 1-3); this
The general properties of animal viruses pathogenic in turn alters the way the proteins interconnect. The exact
for humans are described in Chapter 29. Bacterial viruses, three-dimensional structure of PrPSc is unknown; however,
known as bacterial phages, are described in Chapter 7. it has a higher proportion of β-sheet structures in place of
the normal α-helix structures. Aggregations of PrPSc form
highly structured amyloid fibers, which accumulate to form
PRIONS plaques. It is unclear if these aggregates are the cause of the
cell damage or are simply a side effect of the underlying dis-
A number of remarkable discoveries in the past three ease process. One model of prion replication suggests that
decades have led to the molecular and genetic characteriza- PrPc exists only as fibrils, and that the fibril ends bind PrPc
tion of the transmissible agent causing scrapie, a degenera- and convert it to PrPSc.
tive central nervous system disease of sheep. Studies have There are several prion diseases of importance (Table 1-1
identified a specific protein in preparations from scrapie- and see Chapter 42). Kuru, Creutzfeldt-Jakob disease (CJD),
infected brains of sheep that can reproduce the symptoms Gerstmann-Sträussler-Scheinker disease, and fatal familial
of scrapie in previously uninfected sheep (Figure 1-2). insomnia affect humans. Bovine spongiform encephalopa-
Attempts to identify additional components, such as nucleic thy (BSE), which is thought to result from the ingestion of
acid, have been unsuccessful. To distinguish this agent feeds and bone meal prepared from rendered sheep offal, has
from viruses and viroids, the term prion was introduced been responsible for the deaths of more than 184,000 cattle
to emphasize its proteinaceous and infectious nature. The in Great Britain since its discovery in 1985. A new variant

Riedel_CH01_p001-p010.indd 3 05/04/19 8:37 AM

 4   SECTION I   Fundamentals of Microbiology

Both normal prion protein (NP) and

abnormal prion protein (PP) are present.
PROKARYOTES
PP The primary distinguishing characteristics of the prokary-
otes are their relatively small size, usually on the order of
1 µm in diameter, and the absence of a nuclear membrane.
The DNA of almost all bacteria is a circle which if extended
NP linearly would be about 1 mM; this is the prokaryotic
Step 1 Abnormal prion protein
chromosome. Bacteria are haploid (if multiple copies of
interacts with the normal prion the chromosome are present they are all the same). Most
protein.
prokaryotes have only a single large chromosome that is
organized into a structure known as a nucleoid. The chro-
mosomal DNA must be folded more than 1000-fold just
to fit within the confines of a prokaryotic cell. Substantial
evidence suggests that the folding may be orderly and may
bring specified regions of the DNA into proximity. The
Step 2 The normal prion protein is
converted to the abnormal prion nucleoid can be visualized by electron microscopy as well
PP
protein. as by light microscopy after treatment of the cell to make
the nucleoid visible. Thus, it would be a mistake to con-
Neuron
NP clude that subcellular differentiation, clearly demarcated
by membranes in eukaryotes, is lacking in prokaryotes.
Indeed, some prokaryotes form membrane-bound subcel-
Converted NPs lular structures with specialized function such as the chro-
Steps 3 and 4 The abnormal prion matophores of photosynthetic bacteria (see Chapter 2).
proteins continue to interact with
normal prion proteins
Original until they convert
PP all the normal
prion proteins to
Prokaryotic Diversity
abnormal prion
proteins.
The small size and haploid organization of the prokaryotic
chromosome limits the amount of genetic information it
Converted NP can contain. Recent data based on genome sequencing indi-
cate that the number of genes within a prokaryote may vary
from 468 in Mycoplasma genitalium to 7825 in Streptomyces
coelicolor, and many of these genes must be dedicated to
essential functions such as energy generation, macromolec-
ular synthesis, and cellular replication. Any one prokaryote
carries relatively few genes that allow physiologic accom-
Abnormal prion proteins modation of the organism to its environment. The range of
potential prokaryotic environments is unimaginably broad,
FIGURE 1-3 Proposed mechanism by which prions replicate. and it follows that the prokaryotic group encompasses a het-
The normal and abnormal prion proteins differ in their tertiary erogeneous range of specialists, each adapted to a rather nar-
structure. (Reproduced with permission from Nester EW, Anderson rowly circumscribed niche.
DG, Roberts CE, et al: Microbiology: A Human Perspective, 6th ed. The range of prokaryotic niches is illustrated by con-
McGraw-Hill, 2009, p. 342. © McGraw-Hill Education.)
sideration of strategies used for generation of metabolic
energy. Light from the sun is the chief source of energy for
of CJD (vCJD) has been associated with human ingestion of life. Some prokaryotes such as the purple bacteria convert
prion-infected beef in the United Kingdom and in France. light energy to metabolic energy in the absence of oxygen
A common feature of all of these diseases is the conversion production. Other prokaryotes, exemplified by the blue-
of a host-encoded sialoglycoprotein to a protease-resistant green bacteria (Cyanobacteria), produce oxygen that can
form as a consequence of infection. Recently, an α-synuclein provide energy through respiration in the absence of light.
prion was discovered that caused a neurodegenerative disease Aerobic organisms depend on respiration with oxygen for
called multiple system atrophy in humans. their energy. Some anaerobic organisms can use electron
Human prion diseases are unique in that they manifest acceptors other than oxygen in respiration. Many anaerobes
as sporadic, genetic, and infectious diseases. The study of carry out fermentations in which energy is derived by met-
prion biology is an important emerging area of biomedical abolic rearrangement of chemical growth substrates. The
investigation, and much remains to be learned. tremendous chemical range of potential growth substrates
The general features of the nonliving members of the for aerobic or anaerobic growth is mirrored in the diversity
microbial world are given in Table 1-2. of prokaryotes that have adapted to their utilization.

Riedel_CH01_p001-p010.indd 4 05/04/19 8:37 AM

 CHAPTER 1 The Science of Microbiology   5

TABLE 1-1 Common Human and Animal Prion Diseases

Type Name Etiology

Human prion diseases

Acquired Variant Creutzfeldt-Jakob diseasea Associated with ingestion or inoculation of prion-infected material

Kuru

Iatrogenic Creutzfeldt-Jakob diseaseb

Sporadic Creutzfeldt-Jakob disease Source of infection unknown

Familial Gerstmann-Sträussler-Scheinker Associated with specific mutations within the gene encoding PrP

Fatal familial insomnia

Creutzfeldt-Jakob disease

Animal prion diseases

Cattle Bovine spongiform encephalopathy Exposure to prion-contaminated meat and bone meal

Sheep Scrapie Ingestion of scrapie-contaminated material

Deer, elk Chronic wasting disease Ingestion of prion-contaminated material

Mink Transmissible mink encephalopathy Source of infection unknown

Cats Feline spongiform encephalopathy a

Exposure to prion-contaminated meat and bone meal

PrP, prion protein.

a
Associated with exposure to bovine spongiform encephalopathy-contaminated materials.
b
Associated with prion-contaminated biologic materials, such as dura mater grafts, corneal transplants, and cadaver-derived human growth hormone, or by prion-
contaminated surgical instruments.
Reproduced with permission from the American Society for Microbiology. Priola SA: How animal prions cause disease in humans. Microbe 2008;3(12):568.

Prokaryotic Communities physiologic protection to at least some members of the group.

Extracellular polysaccharides, for example, may afford pro-
A useful survival strategy for specialists is to enter into
tection against potentially lethal agents such as antibiotics
consortia, arrangements in which the physiologic charac-
or heavy metal ions. Large amounts of polysaccharides pro-
teristics of different organisms contribute to survival of the
duced by the high number of cells within a clone may allow
group as a whole. If the organisms within a physically inter-
cells within the interior to survive exposure to a lethal agent
connected community are directly derived from a single cell,
at a concentration that might kill single cells.
the community is a clone that may contain up to 108 or greater
Many bacteria exploit a cell–cell communication mech-
cells. The biology of such a community differs substantially
anism called quorum sensing to regulate the transcription
from that of a single cell. For example, the high cell number
of genes involved in diverse physiologic processes, including
virtually ensures the presence within the clone of at least one
bioluminescence, plasmid conjugal transfer, and the produc-
cell carrying a variant of any gene on the chromosome. Thus,
tion of virulence determinants. Quorum sensing depends on
genetic variability—the wellspring of the evolutionary pro-
the production of one or more diffusible signal molecules
cess called natural selection—is ensured within a clone. The
(eg, acetylated homoserine lactone [AHL]) termed autoin-
high number of cells within clones is also likely to provide
ducers or pheromones that enable a bacterium to monitor
its own cell population density (Figure 1-4). The coopera-
TABLE 1-2 Distinguishing Characteristics of Viruses, tive activities leading to biofilm formation are controlled by
Viroids, and Prions quorum sensing. It is an example of multicellular behavior in
Viruses Viroids Prions prokaryotes.
Another distinguishing characteristic of prokaryotes is
Obligate intracellular Obligate Abnormal form of a
agents intracellular cellular protein
their capacity to exchange small packets of genetic information.
agents This information may be carried on plasmids, small and spe-
cialized genetic elements that are capable of replication within
Consist of either DNA Consist only Consist only of
or RNA surrounded of RNA; no protein; no DNA at least one prokaryotic cell line. In some cases, plasmids may
by a protein coat protein coat or RNA be transferred from one cell to another and thus may carry sets
of specialized genetic information through a population. Some
Reproduced with permission from Nester EW, Anderson DG, Roberts CE, et al:
Microbiology: A Human Perspective, 6th ed. McGraw-Hill, 2009, p. 13. © McGraw-Hill
plasmids exhibit a broad host range that allows them to con-
Education. vey sets of genes to diverse organisms. Of particular concern

Riedel_CH01_p001-p010.indd 5 05/04/19 8:37 AM

 6   SECTION I   Fundamentals of Microbiology

Bacterial cell Signaling

molecule

When few cells are present, the When many cells are present, the
concentration of the signaling concentration of the AHL is high.
molecule acylated homoserine High concentrations of AHL induce
lactone (AHL) is low. expression of specific genes.

FIGURE 1-4 Quorum sensing. (Reproduced with permission from Nester EW, Anderson DG, Roberts CE, et al: Microbiology: A Human
Perspective, 6th ed. McGraw-Hill, 2009, p. 181. © McGraw-Hill Education.)

are drug resistance plasmids that may render diverse bacteria allows a scientist to choose characteristics that allow swift
resistant to antibiotic treatment (Chapter 7). and accurate categorization of a newly encountered organ-
The survival strategy of a single prokaryotic cell line may ism. This categorical organization allows prediction of
lead to a range of interactions with other organisms. These many additional traits shared by other members of the
may include symbiotic relationships illustrated by complex category. In a hospital setting, successful classification of
nutritional exchanges among organisms within the human a pathogenic organism may provide the most direct route
gut. These exchanges benefit both the microorganisms and to its elimination. Classification may also provide a broad
their human host. Parasitic interactions can be quite delete- understanding of relationships among different organ-
rious to the host. Advanced symbiosis or parasitism can lead isms, and such information may have great practical value.
to loss of functions that may not allow growth of the symbi- For example, elimination of a pathogenic organism will be
ont or parasite independent of its host. relatively long-lasting if its habitat is occupied by a non-
The mycoplasmas, for example, are parasitic prokaryotes pathogenic variant.
that have lost the ability to form a cell wall. Adaptation of these The principles of prokaryotic classification are discussed
organisms to their parasitic environment has resulted in incor- in Chapter 3. At the outset, it should be recognized that any
poration of a substantial quantity of cholesterol into their cell prokaryotic characteristic might serve as a potential criterion
membranes. Cholesterol, not found in other prokaryotes, is for classification. However, not all criteria are equally effec-
assimilated from the metabolic environment provided by the tive in grouping organisms. Possession of DNA, for example,
host. Loss of function is exemplified also by obligate intracel- is a useless criterion for distinguishing organisms because all
lular parasites, the chlamydiae and rickettsiae. These bacteria cells contain DNA. The presence of a broad host range plas-
are extremely small (0.2–0.5 µm in diameter) and depend on mid is not a useful criterion because such plasmids may be
the host cell for many essential metabolites and coenzymes. found in diverse hosts and need not be present all of the time.
This loss of function is reflected by the presence of a smaller Useful criteria may be structural, physiologic, biochemical,
genome with fewer genes (see Table 7-1). or genetic. Spores—specialized cell structures that may allow
The most widely distributed examples of bacterial survival in extreme environments—are useful structural cri-
symbionts appear to be chloroplasts and mitochondria, the teria for classification because well-characterized subsets of
energy-yielding organelles of eukaryotes. Evidence points to bacteria form spores. Some bacterial groups can be effectively
the conclusion that ancestors of these chloroplasts and mito- subdivided based upon their ability to ferment specified car-
chondria were endosymbionts, essentially “domesticated bohydrates. Such criteria may be ineffective when applied to
bacteria” that established symbiosis within the cell mem- other bacterial groups that may lack any fermentative capa-
brane of the ancestral eukaryotic host. The presence of mul- bility. A biochemical test, the Gram-stain, is an effective cri-
tiple copies of these organelles may have contributed to the terion for classification because response to the stain reflects
relatively large size of eukaryotic cells and to their capacity fundamental differences in the bacterial cell envelope that
for specialization, a trait ultimately reflected in the evolution divide most bacteria into two major groups.
of differentiated multicellular organisms. Genetic criteria are increasingly used in bacterial clas-
sification, and many of these advances are made possible
by the development of DNA-based technologies. It is now
Classification of the Prokaryotes possible to design DNA probe or DNA amplification assays
An understanding of any group of organisms requires (eg, polymerase chain reaction [PCR] assays) that swiftly
their classification. An appropriate classification system identify organisms carrying specified genetic regions with

Riedel_CH01_p001-p010.indd 6 05/04/19 8:37 AM

 CHAPTER 1 The Science of Microbiology   7

common ancestry. Comparison of DNA sequences for some through a series of events achieving physiologic integration
genes has led to the elucidation of phylogenetic relation- of the nucleus with the endoplasmic reticulum, a structure
ships among prokaryotes. Ancestral cell lines can be traced, that has no counterpart in prokaryotes. Eukaryotes are set
and organisms can be grouped based on their evolution- apart by the organization of their cellular DNA in chromo-
ary affinities. These investigations have led to some strik- somes separated by a distinctive mitotic apparatus during cell
ing conclusions. For example, comparison of cytochrome c division.
sequences suggests that all eukaryotes, including humans, In general, genetic transfer among eukaryotes depends
arose from one of three different groups of purple photo- on fusion of haploid gametes to form a diploid cell con-
synthetic bacteria. This conclusion in part explains the evo- taining a full set of genes derived from each gamete. The
lutionary origin of eukaryotes, but it does not fully take into life cycle of many eukaryotes is almost entirely in the dip-
account the generally accepted view that the eukaryotic cell loid state, a form not encountered in prokaryotes. Fusion
was derived from the evolutionary merger of different pro- of gametes to form reproductive progeny is a highly spe-
karyotic cell lines. cific event and establishes the basis for eukaryotic species.
This term can be applied only metaphorically to the pro-
karyotes, which exchange fragments of DNA through
Bacteria and Archaebacteria: The Major recombination. Currently, the term protist is used infor-
Subdivisions Within the Prokaryotes mally as a catch-all term for unicellular eukaryotic micro-
A major success in molecular phylogeny has been the dem- organisms. Because protists as a whole are paraphyletic,
onstration that prokaryotes fall into two major groups. newer classification systems often split up traditional sub-
Most investigations have been directed to one group, the divisions or groups based on morphological or biochemi-
bacteria. The other group, the archaebacteria, has received cal characteristics.
relatively little attention until recently, partly because many Traditionally, microbial eukaryotes—protists—are
of its representatives are difficult to study in the laboratory. placed in one of the four following major groups: algae,
Some archaebacteria, for example, are killed by contact with protozoa, fungi, and slime molds. These traditional sub-
oxygen, and others grow at temperatures exceeding that of divisions, largely based on superficial commonalities,
boiling water. Before molecular evidence became available, have been largely replaced by classification schemes based
the major subgroupings of archaebacteria had seemed dis- on phylogenetics. Molecular methods used by modern
parate. The methanogens carry out an anaerobic respiration taxonomists have been used to generate data support-
that gives rise to methane, the halophiles demand extremely ing the redistribution of some members of these groups
high salt concentrations for growth, and the thermoacido- into diverse and sometimes distantly related phyla. For
philes require high temperature and acidity for growth. It has example, the water molds are now considered to be closely
now been established that these prokaryotes share biochemi- related to photosynthetic organisms such as brown algae
cal traits such as cell wall or membrane components that and diatoms.
set the group entirely apart from all other living organisms.
An intriguing trait shared by archaebacteria and eukary-
otes is the presence of introns within genes. The function
Algae
of introns—segments of DNA that interrupts informational The term algae has long been used to denote all organisms
DNA within genes—is not established. What is known is that produce O2 as a product of photosynthesis. One for-
that introns represent a fundamental characteristic shared mer subgroup of these organisms—the blue-green algae, or
by the DNA of archaebacteria and eukaryotes. This common cyanobacteria—are prokaryotic and no longer are termed
trait has led to the suggestion that—just as mitochondria algae. This classification is reserved exclusively for a large
and chloroplasts appear to be evolutionary derivatives of the diverse group of photosynthetic eukaryotic organisms. For-
bacteria—the eukaryotic nucleus may have arisen from an merly, all algae were thought to contain chlorophyll in the
archaebacterial ancestor. photosynthetic membrane of their chloroplast, a subcellu-
lar organelle that is similar in structure to cyanobacteria.
Modern taxonomic approaches have recognized that some
PROTISTS algae lack chlorophyll and have a free-living heterotrophic
or parasitic life style. Many algal species are unicellular
The “true nucleus” of eukaryotes (from Gr karyon, “nucleus”) microorganisms. Other algae may form extremely large
is only one of their distinguishing features. The membrane- multicellular structures. Kelps of brown algae sometimes
bound organelles, the microtubules, and the microfilaments are several hundred meters in length. Several algae produce
of eukaryotes form a complex intracellular structure unlike toxins that are poisonous to humans and other animals.
that found in prokaryotes. The organelles responsible for Dinoflagellates, a unicellular alga, are responsible for algal
the motility of eukaryotic cells are flagella or cilia—complex blooms, or red tides, in the ocean (Figure 1-5). Red tides
multistranded structures that do not resemble the flagella caused by the dinoflagellate Gonyaulax species are serious
of prokaryotes. Gene expression in eukaryotes takes place because this organism produces potent neurotoxins such as

Riedel_CH01_p001-p010.indd 7 05/04/19 8:37 AM

 8   SECTION I   Fundamentals of Microbiology

are known that have flagella at one stage in their life cycle
and pseudopodia at another stage. A fourth major group of
protozoa, the sporozoa, are strict parasites that are usually
nonmotile; most of these reproduce sexually and asexually
in alternate generations by means of spores. Recent taxo-
nomic studies have shown that only the ciliates are mono-
phyletic, that is, a distinct lineage of organisms sharing
common ancestry. The other classes of protozoa are all
polyphyletic groups made up of organisms that, despite
similarities in appearance (eg, flagellates) or way of life
(eg, endoparasitic), are not necessarily closely related to
one another. Protozoan parasites of humans are discussed
in Chapter 46.

Fungi
The fungi are nonphotosynthetic protists that may or may not
grow as a mass of branching, interlacing filaments (“hyphae”)
known as a mycelium. If a fungus grows simply as a single
cell it is called a yeast. If mycelial growth occurs, it is called
FIGURE 1-5 The dinoflagellate Gymnodinium scanning electron a mold. Most fungi of medical importance grow dimorphi-
micrograph (4000×). (Reproduced with permission from Dr. David cally, that is, they exist as a mold at room temperature but as
Phillips/Visuals Unlimited.) a yeast at body temperature. Remarkably, the largest known
contiguous fungal mycelium covered an area of 2400 acres
(9.7 km2) at a site in eastern Oregon. Although the hyphae
saxitoxin and gonyautoxins, which accumulate in shellfish exhibit cross walls, the cross walls are perforated and allow
(eg, clams, mussels, scallops, and oysters) that feed on this free passage of nuclei and cytoplasm. The entire organism is
organism. Ingestion of these shellfish by humans results in thus a coenocyte (a multinucleated mass of continuous cyto-
symptoms of paralytic shellfish poisoning and can lead to plasm) confined within a series of branching tubes. These
death. Some algae (eg, Prototheca and Helicosporidium) are tubes, made of polysaccharides such as chitin, are homolo-
parasites of metazoans or plants. Protothecosis is a disease gous with cell walls.
of dogs, cats, cattle, and rarely humans caused by a type of The fungi probably represent an evolutionary offshoot
algae, Prototheca, that lacks chlorophyll. The two most com- of the protozoa; they are unrelated to the actinomycetes,
mon species are P. wickerhamii and P. zopfii; most human mycelial bacteria that they superficially resemble. The
cases, which are associated with a defective immune system, major subdivisions (phyla) of fungi are Chytridiomycota,
are caused by P. wickerhamii. Zygomycota (the zygomycetes), Ascomycota (the asco-
mycetes), Basidiomycota (the basidiomycetes), and the
“deuteromycetes” (or imperfect fungi). The evolution of the
Protozoa ascomycetes from the phycomycetes is seen in a transitional
Protozoa is an informal term for single-celled nonphoto- group, whose members form a zygote but then transform
synthetic eukaryotes that are either free-living or para- this directly into an ascus. The basidiomycetes are believed
sitic. Protozoa are abundant in aqueous environments to have evolved in turn from the ascomycetes. The classifi-
and soil. They range in size from as little as 1µm to sev- cation of fungi and their medical significance are discussed
eral millimeters, or more. All protozoa are heterotrophic, further in Chapter 45.
deriving nutrients from other organisms, either by ingest-
ing them whole or by consuming their organic tissue or
waste products. Some protozoans take in food by phago- Slime Molds
cytosis, engulfing organic particles with pseudopodia (eg, These organisms are characterized by the presence, as a
amoeba), or taking in food through a mouth-like aperture stage in their life cycle, of an ameboid multinucleate mass
called a cytostome. Other protozoans absorb dissolved of cytoplasm called a plasmodium. The plasmodium of a
nutrients through their cell membranes, a process called slime mold is analogous to the mycelium of a true fungus.
osmotrophy. Both are coenocytic. Whereas in the latter, cytoplasmic flow
Historically, the major groups of protozoa included: is confined to the branching network of chitinous tubes, in
flagellates, motile cells possessing whip-like organelles of the former, the cytoplasm can flow in all directions. This
locomotion; amoebae, cells that move by extending pseu- flow causes the plasmodium to migrate in the direction of
dopodia; and ciliates, cells possessing large numbers of its food source, frequently bacteria. In response to a chemi-
short hair-like organelles of motility. Intermediate forms cal signal, 3′, 5′-cyclic AMP, the plasmodium, which reaches

Riedel_CH01_p001-p010.indd 8 05/04/19 8:37 AM

 CHAPTER 1 The Science of Microbiology   9

Spores

Fruiting bodies
Germination
release spores

Myxamoebae

Fruiting body

Plasmodium

A B

FIGURE 1-6 Slime molds. A: Life cycle of an acellular slime mold. B: Fruiting body of a cellular slime mold. (Reproduced with permission
from Carolina Biological Supply/DIOMEDIA.)

macroscopic size, differentiates into a stalked body that can REVIEW QUESTIONS
produce individual motile cells. These cells, flagellated or
1. Which one of the following terms characterizes the interaction
ameboid, initiate a new round in the life cycle of the slime
between herpes simplex virus and a human?
mold (Figure 1-6). The cycle frequently is initiated by sexual
(A) Parasitism
fusion of single cells.
(B) Symbiosis
The growth of slime molds depends on nutrients pro-
(C) Endosymbiosis
vided by bacterial or, in some cases, plant cells. Reproduction (D) Endoparasitism
of the slime molds via plasmodia can depend on intercellular (E) Consortia
recognition and fusion of cells from the same species. The 2. Which one of the following agents lacks nucleic acid?
life cycle of the slime molds illustrates a central theme of this
(A) Bacteria
chapter—the interdependency of living forms. Full under- (B) Viruses
standing of any microorganism requires both knowledge of (C) Viroids
the other organisms with which it coevolved and an apprecia- (D) Prions
tion of the range of physiologic responses that may contribute (E) Protozoa
to survival. 3. Which one of the following is a prokaryote?
(A) Bacteria
(B) Algae
CHAPTER SUMMARY (C) Protozoa
(D) Fungi
• Microorganisms are a large and diverse group of organisms (E) Slime molds
existing as single cells or clusters; they also include viruses, 4. Which one of the following agents simultaneously contains
which are microscopic but not cellular. both DNA and RNA?
• A virus consists of a nucleic acid molecule, either DNA (A) Bacteria
or RNA, enclosed in a protein coat, or capsid, sometimes (B) Viruses
enclosed by an envelope composed of lipids, proteins, and (C) Viroids
carbohydrates. (D) Prions
• A prion is an infectious protein, which is capable of causing (E) Plasmids
chronic neurologic diseases. 5. Which of the following cannot be infected by viruses?
• Prokaryotes consist of bacteria and archaebacteria. (A) Bacteria
• Prokaryotes are haploid. (B) Protozoa
• Microbial eukaryotes, or protists, are members of four (C) Human cells
major groups: algae, protozoa, fungi, and slime molds. (D) Viruses
• Eukaryotes have a true nucleus and are diploid. (E) None of the above

Riedel_CH01_p001-p010.indd 9 05/04/19 8:37 AM

 10   SECTION I   Fundamentals of Microbiology

6. Viruses, bacteria, and protists are uniquely characterized by Answers

their respective size. True or false?
1. A 5. E 9. D
(A) True 2. D 6. B 10. C
(B) False
3. A 7. E
7. Quorum sensing in prokaryotes involves 4. A 8. D
(A) Cell–cell communication
(B) Production of molecules such as AHL
(C) An example of multicellular behavior
(D) Regulation of genes involved in diverse physiologic
REFERENCES
processes Abrescia NGA, Bamford DH, Grimes JM, et al: Structure unifies
(E) All of the above the viral universe. Annu Rev Biochem 2012;81:795.
8. A 16-year-old female patient presented to her family physi- Adi SM, Simpson AGB, Lane CE, et al: The revised classification of
cian with a complaint of an abnormal vaginal discharge and eukaryotes. J Eukaryot Microbiol 2012;59:429.
pruritus (itching). The patient denied having sexual activity Arslan D, Legendre M, Seltzer V, et al: Distant Mimivirus relative
and recently completed a course of doxycycline for the treat- with a larger genome highlights the fundamental features of
ment of her acne. An examination of a Gram-stained vaginal Megaviridae. Proc Natl Acad Sci U S A 2011;108:17486.
smear revealed the presence of Gram-positive oval cells about Belay ED: Transmissible spongiform encephalopathies in humans.
4–8 µm in diameter. Her vaginitis is caused by which of the Annu Rev Microbiol 1999;53:283.
following agents? Colby DW, Prusiner SB: De novo generation of prion strains.
Nat Rev Microbiol 2011;9:771.
(A) Bacterium
Diener TO: Viroids and the nature of viroid diseases. Arch Virol
(B) Virus
1999;15(Suppl):203.
(C) Protozoa
Fournier PE, Raoult D: Prospects for the future using genomics
(D) Fungus
and proteomics in clinical microbiology. Annu Rev Microbiol
(E) Prion
2011;65:169.
9. A 65-year-old man develops dementia, progressive over several Katz LA: Origin and diversification of eukaryotes. Annu Rev
months, along with ataxia and somnolence. An electroencepha- Microbiol 2012;63:411.
lographic pattern shows paroxysms with high voltages and slow Lederberg J (editor): Encyclopedia of Microbiology, 4 vols.
waves, suggestive of CJD. By which of the following agents is Academic Press, 1992.
this disease caused? Olsen GJ, Woese CR: The winds of (evolutionary) change: Breath-
(A) Bacterium ing new life into microbiology. J Bacteriol 1994;176:1.
(B) Virus Priola SA: How animal prions cause disease in humans. Microbe
(C) Viroid 2008;3:568.
(D) Prion Prusiner SB: Biology and genetics of prion diseases. Annu Rev
(E) Plasmid Microbiol 1994;48:655.
10. Twenty minutes after ingesting a raw clam, a 35-year-old man Prusiner SB, Woerman AL, Mordes DA, et al: Evidence for
experiences paresthesias of the mouth and extremities, head- α-synuclein prions causing multiple system atrophy in
ache, and ataxia. These symptoms are the result of a neurotoxin humans with parkinsonism. Proc Natl Acad Sci U S A
produced by algae called 2015;112:E5308-E5317.
(A) Amoeba Schloss PD, Handlesman J: Status of the microbial census.
(B) Blue-green algae Microbiol Mol Biol Rev 2004;68:686.
(C) Dinoflagellates Sleigh MA: Protozoa and Other Protists. Chapman & Hall, 1990.
(D) Kelp Whitman WB, Coleman DC, Wiebe WJ: Prokaryotes: The unseen
(E) None of the above majority. Proc Natl Acad Sci U S A 1998;95:6578.

Riedel_CH01_p001-p010.indd 10 05/04/19 8:37 AM

 2
C H A P T E R

Cell Structure

This chapter discusses the basic structure and function of the B. Phase-Contrast Microscope
components that make up eukaryotic and prokaryotic cells. It The phase-contrast microscope was developed to improve
begins with a discussion of the microscope. Historically, the contrast differences between cells and the surrounding
microscope first revealed the presence of bacteria and later medium, making it possible to see living cells without stain-
the secrets of cell structure. Today, it remains a powerful tool ing them; with bright-field microscopes, killed and stained
in cell biology. preparations must be used. The phase-contrast microscope
takes advantage of the fact that light waves passing through
transparent objects, such as cells, emerge in different phases
OPTICAL METHODS depending on the properties of the materials through which
they pass. This effect is amplified by a special ring in the
The Light Microscope objective lens of a phase-contrast microscope, leading to the
The resolving power of the light microscope under ideal con- formation of a dark image on a light background (Figure 2-1).
ditions is about half the wavelength of the light being used.
(Resolving power is the distance that must separate two C. Dark-Field Microscope
point sources of light if they are to be seen as two distinct The dark-field microscope is a light microscope in which
images.) With yellow light of a wavelength of 0.4 µm, the the lighting system has been modified to reach the speci-
smallest separable diameters are thus about 0.2 µm (ie, one- men from the sides only. This is accomplished through the
third the width of a typical prokaryotic cell). The useful mag- use of a special condenser that both blocks direct light rays
nification of a microscope is the magnification that makes and deflects light off a mirror on the side of the condenser
visible the smallest resolvable particles. Several types of light at an oblique angle. This creates a “dark field” that contrasts
microscopes, which are commonly used in microbiology, are against the highlighted edge of the specimens and results
discussed as follows. when the oblique rays are reflected from the edge of the spec-
imen upward into the objective of the microscope. Resolution
A. Bright-Field Microscope by dark-field microscopy is quite high. Thus, this technique
The bright-field microscope is the most commonly used in has been particularly useful for observing organisms such as
microbiology courses and consists of two series of lenses Treponema pallidum, a spirochete that is smaller than 0.2 µm
(objective and ocular lens), which function together to in diameter and therefore cannot be observed with a bright-
resolve the image. These microscopes generally employ a field or phase-contrast microscope (Figure 2-2A).
100-power objective lens with a 10-power ocular lens, thus
magnifying the specimen 1000 times. Particles 0.2 µm in D. Fluorescence Microscope
diameter are therefore magnified to about 0.2 mm and so The fluorescence microscope is used to visualize specimens
become clearly visible. Further magnification would give no that fluoresce, which is the ability to absorb short wave-
greater resolution of detail and would reduce the visible area lengths of light (ultraviolet) and give off light at a longer wave-
(field). length (visible). Some organisms fluoresce naturally because
With this microscope, specimens are rendered visible of the presence within the cells of naturally fluorescent sub-
because of the differences in contrast between them and stances such as chlorophyll. Those that do not naturally fluo-
the surrounding medium. Many bacteria are difficult to resce may be stained with a group of fluorescent dyes called
see well because of their lack of contrast with the surround- fluorochromes. Fluorescence microscopy is widely used in
ing medium. Dyes (stains) can be used to stain cells or their clinical diagnostic microbiology. For example, the fluoro-
organelles and increase their contrast so that they can be chrome auramine O, which glows yellow when exposed to
more easily seen in the bright-field microscope. ultraviolet light, is strongly absorbed by the cell envelope of

11

Riedel_CH02_p011-p042.indd 11 05/04/19 1:56 PM