Infectious Disease Diagnosis

Proper diagnosis of infectious illnesses is essential for both appropriate treatment of

patients and carrying out prevention and control surveillance activities. Two important
properties that should be considered for any diagnostic test utilized are sensitivity and
specificity. Sensitivity refers to the ability of the test to correctly identify individuals
infected with an agent (‘positive in disease’). A test that is very sensitive is more likely
to pick up individuals with the disease (and possibly some without the disease); a very
sensitive test will have few false negatives. Specificity is the ability of the test to
correctly identify individuals not infected by a particular agent (‘negative in health’);
high specificity implies few false positives. Often, screening tests are highly sensitive
(to capture any possible cases), and confirmatory tests are more specific (to rule out
false-positive screening tests).

Broadly, laboratory diagnosis of infectious diseases is based on tests that either directly
identify an infectious agent or provide evidence that infection has occurred by
documenting agent-specific immunity in the host. Identification of an infecting agent
involves either direct examination of host specimens (e.g., blood, tissue, urine) or
environmental specimens, or examination following agent culture and isolation from
such specimens. The main categories of analyses used in pathogen identification can be
classified as phenotypic, revealing properties of the intact agent, nucleic acid-based,
determining agent nucleic acid (DNA or RNA) characteristics and composition,
and immunologic, detecting microbial antigen or evidence of immune response to an
agent. Direct phenotypic analyses include both macroscopic and/or microscopic
examination of specimens to determine agent morphology and staining properties.
Cultured material containing large quantities of agent can undergo analyses to
determine characteristics, such as biochemical enzymatic activity (enzymatic profile)
and antimicrobial sensitivity, and to perform phage typing, a technique which
differentiates bacterial strains according to the infectivity of strain-specific bacterial
viruses (a.k.a. bacteriophages). Nucleic acid–based tests often make use of
the polymerase chain reaction (PCR) to amplify agent DNA or complementary DNA
(cDNA) synthesized from messenger RNA (mRNA). The ability of pathogen-specific
PCR primers to generate an amplification product can confirm or rule out involvement
of a specific pathogen. Sequencing of amplified DNA fragments can also assist with
pathogen identification. Restriction fragment analysis, as by pulse-field gel
electrophoresis of restriction enzyme-digested genomic DNA isolated from cultured
material, can yield distinct ‘DNA fingerprints’ that can be used for comparing the
identities of bacteria. The CDC PulseNet surveillance program uses DNA
fingerprinting as the basis for detecting and defining foodborne disease outbreaks that
can sometimes be quite widely dispersed (CDC, 2013). Most recently, next-generation
sequencing technologies have made whole-genome sequencing a realistic subtyping
method for use in foodborne outbreak investigation and surveillance (Deng et al., 2016).
The objective of immunologic analysis of specimens is to reveal evidence of an agent
through detection of its antigenic components with agent-specific
antibodies. Serotyping refers to the grouping of variants of species of bacteria or viruses
based on shared surface antigens that are identified using immunologic methodologies
such as enzyme-linked immunosorbent assay (ELISA) and Western blotting.
Methods of infectious disease diagnosis. Laboratory methods for infectious disease
diagnosis focus on either analyzing host specimens or environmental samples for an
agent (upper section), or analyzing the host for evidence of immunity to an agent (lower
section). Closed solid bullets, category of test; open bullets, examples of tests. PCR,
polymerase chain reaction; ELISA, enzyme-linked immunosorbent assay; PFGE,
pulsed-field gel electrophoresis.

Immunologic assays are also used to look for evidence that an agent-specific immune
response has occurred in an exposed or potentially exposed individual. Serologic tests
detect pathogen-specific B cell–secreted antibodies in serum or other body fluids. Some
serologic assays simply detect the ability of host antibodies to bind to killed pathogen or
components of pathogen (e.g., ELISA). Others rely on the ability of antibodies to
actually neutralize the activity of live microbes; as, for example, the plaque reduction
neutralization test which determines the ability of serum antibodies to neutralize
virus. Antibody titer measures the amount of a specific antibody present in serum or
other fluid, expressed as the greatest dilution of serum that still gives a positive test in
whatever assay is being employed. Intradermal tests for identification of T cell–
mediated immediate type (Type I) hypersensitivity or delayed type (Type IV)
hypersensitivity responses to microbial antigen can be used to diagnose or support the
diagnosis of some bacterial, fungal, and parasitic infections, such as, the Mantoux
(tuberculin) test for TB.
Infectious Disease Control and Prevention

Based on the classic model of Leavell and Clark (1965), infectious

disease prevention activities can be categorized as primary, secondary, or
tertiary. Primary prevention occurs at the predisease phase and aims to protect
populations, so that infection and disease never occur. For example, measles
immunization campaigns aim to decrease susceptibility following exposure. The goal
of secondary prevention is to halt the progress of an infection during its early, often
asymptomatic stages so as to prevent disease development or limit its severity; steps
important for not only improving the prognosis of individual cases but also preventing
infectious agent transmission. For example, interventions for secondary prevention of
hepatitis C in injection drug user populations include early diagnosis and treatment by
active surveillance and screening (Miller and Dillon, 2015). Tertiary prevention focuses
on diseased individuals with the objective of limiting impact through, for example,
interventions that decrease disease progression, increase functionality, and maximize
quality of life. Broadly, public health efforts to control infectious diseases focus on
primary and secondary prevention activities that reduce the potential for exposure to an
infectious agent and increase host resistance to infection. The objective of these
activities can extend beyond disease control, as defined by the 1997 Dahlem Workshop
on the Eradication of Infectious Diseases, to reach objectives
of elimination and eradication (Dowdle, 1998; Box 1 ).
Box 1. Hierarchy of public health efforts targeting
infectious diseases.
The 1997 Dahlem Workshop on the Eradication of Infectious Diseases defined a
continuum of outcomes due to public health interventions targeting infectious diseases:
“1) control, the reduction of disease incidence, prevalence, morbidity or mortality to a
locally acceptable level as a result of deliberate efforts; continued intervention measures
are required to maintain the reduction (e.g. diarrheal diseases), 2) elimination of
disease, reduction to zero of the incidence of a specified disease in a defined
geographical area as a result of deliberate efforts; continued intervention measures are
required (e.g. neonatal tetanus), 3) elimination of infections, reduction to zero of the
incidence of infection caused by a specific agent in a defined geographical area as a
result of deliberate efforts; continued measures to prevent re-establishment of
transmission are required (e.g. measles, poliomyelitis),4) eradication, permanent
reduction to zero of the worldwide incidence of infection caused by a specific agent as a
result of deliberate efforts; intervention measures are no longer needed (e.g. smallpox),
and 5) extinction, the specific infectious agent no longer exists in nature or in the
laboratory (e.g. none)” (Dowdle, 1998).

As noted earlier, the causation and spread of an infectious disease is determined by the
interplay between agent, host, and environmental factors. For any infectious disease,
this interplay requires a specific linked sequence of events termed the chain of
infection or chain of transmission (Figure 6 ). The chain starts with the infectious
agent residing and multiplying in some natural reservoir; a human, animal, or part of
the environment such as soil or water that supports the existence of the infectious agent
in nature. The infectious agent leaves the reservoir via a portal of exit and, using
some mode of transmission, moves to reach a portal of entry into a susceptible host. A
thorough understanding of the chain of infection is crucial for the prevention and
control of any infectious disease, as breaking a link anywhere along the chain will stop
transmission of the infectious agent. Often more than one intervention can be effective
in controlling a disease, and the approach selected will depend on multiple factors such
as economics and ease with which an intervention can be executed in a given setting. It
is important to realize that the potential for rapid and far-reaching movement of
infectious agents that has accompanied globalization means that coordination of
intervention activities within and between nations is required for optimal prevention and
control of certain diseases.

The chain of infection (a.k.a. chain of transmission). One way to visualize the
transmission of an infectious agent though a population is through the
interconnectedness of six elements linked in a chain. Public health control and
prevention efforts focus on breaking one or more links of the chain in order to stop
disease spread.
The Infectious Agent and Its Reservoir

The cause of any infectious disease is the infectious agent. As discussed earlier, many
types of agents exist, and each can be characterized by its traits of infectivity,
pathogenicity, and virulence. A reservoir is often, but not always, the source from
which the agent is transferred to a susceptible host. For example, bats are both the
reservoir for Marburg virus and a source of infection for humans and bush animals
including African gorillas. However, because morbidity and mortality due to Marburg
infection is significant among these bush animals, they cannot act as a reservoir to
sustain the virus in nature (they die too quickly), although they can act as a source to
transmit Marburg to humans.

Infectious agents can exist in more than one type of reservoir. The number and types of
reservoirs are important determinants of how easily an infectious disease can be
prevented, controlled, and, in some cases, eliminated or eradicated. Animal, particularly
wild animal, reservoirs, and environmental reservoirs in nature can be difficult to
manage and, thus, can pose significant challenges to public health control efforts. In
contrast, infectious agents that only occur in human reservoirs are among those most
easily targeted, as illustrated by the success of smallpox eradication.

Humans are the reservoir for many common infectious diseases including STIs (e.g.,
HIV, syphilis) and respiratory diseases (e.g., influenza). Humans also serve as a
reservoir, although not always a primary reservoir, for many neglected tropical
diseases (NTDs) as, for example, dracunculiasis (a.k.a. Guinea worm). From a public
health standpoint, an important feature of human reservoirs is that they might not show
signs of illness and, thus, can potentially act as unrecognized carriers of disease within
communities. The classic example of a human reservoir is the cook Mary Mallon
(Typhoid Mary); an asymptomatic chronic carrier of Salmonella enterica serovar Typhi
who was linked to at least 53 cases of typhoid fever (Soper, 1939).

Animals are a reservoir for many human infectious diseases. Zoonosis is the term used
to describe any infectious disease that is naturally transmissible from animals to
humans. These diseases make up approximately 60% of all infectious diseases, and an
estimated 75% of recently emerging infectious diseases (Burke et al., 2012). Zoonotic
reservoirs and sources of human disease agents include both domestic (companion and
production) animals (e.g., dogs and cows) and wildlife. Control and prevention of
zoonotic diseases requires the concerted efforts of professionals of multiple disciplines
and is the basis for what has become known as the One Health approach (Gibbs, 2014).
This approach emphasizes the interconnectedness of human health, animal health, and
the environment and recognizes the necessity of multidisciplinary collaboration in order
to prevent and respond to public health threats.

Inanimate matter in the environment, such as soil and water, can also act as a reservoir
of human infectious disease agents. The causative agents of tetanus and botulism
(Clostridium tetani and C. botulinum) are examples of environmental pathogens that
can survive for years within soil and still remain infectious to humans. Legionella
pneumophila, the etiologic agent of Legionnaires' disease, is part of the natural flora of
freshwater rivers, streams, and other bodies. However, the pathogen particularly thrives
in engineered aquatic reservoirs such as cooling towers, fountains, and central air
conditioning systems, which provide conditions that promote bacterial multiplication
and are frequently linked to outbreaks. Soil and water are also sources of infection for
several protozoa and helminth species which, when excreted by a human reservoir host,
can often survive for weeks to months. Outbreaks of both cryptosporidiosis and
giardiasis commonly occur during summer months as a result of contact with
contaminated recreational water. Soil containing roundworm (Ascaris lumbricoides)
eggs is an important source of soil-transmitted helminth infections in children.