15.1 Introduction
A large majority of microorganisms are completely harmless
and play essential functions in ecosystems as well as in
human life sustaining. Nevertheless, some microorganisms,
called pathogens*, can cause diseases of varying severity
in humans and animals. Human pathogens are relatively
diverse, belonging to viruses, bacteria, fungi, protozoa, and
algae. They may be present in many different environments
such as water, soil, gastrointestinal tract, and air. The contamination of water by pathogenic microorganisms arguably
represents one of the most significant risks for human health
on a global scale, and there have been numerous cases of
poisoning and disease outbreaks throughout history resulting
directly of poorly treated or untreated water. Water-related
diseases are a major cause of morbidity and mortality worldwide, and contamination of drinking water remains a significant problem, even in OECD countries. Improving the
quality of drinking water is a major public health concern
for the twenty-first century. Moreover, monitoring of drinking water quality is part of a broad control of the microbiological quality of water systems, including groundwater
and surface water (freshwaters and marine waters), which
are increasingly used as drinking water supply. If the health
problems associated with direct consumption of poor water
quality are by far the most important concerns, it is also
important to consider the quality of surface waters used for
irrigation of agricultural lands, aquaculture, and recreation.
The availability of reliable, easy to use, and effective
methods is crucial to ensure the microbiological safety of
water. Whatever the method used, cultivation or direct observation, the great variety of pathogenic microorganisms does not
allow the search for all pathogens and requires the use of “pollution indicators” such as fecal bacteria (e.g., Escherichia coli and
enterococci). Moreover, culture-based methods are timeconsuming, and when they are used to enumerate indicators or
pathogenic bacteria, the time required to obtain a diagnostic is
often too long to protect people from contamination. As an
example, at least 4–5 days are required to diagnose the presence
of Salmonella spp. or Legionella spp. in water samples by
culture processes. The use of the fecal bacteria indicators has
been very helpful in reducing cases of cholera and typhoid and
to protect against pathogenic bacteria such as Salmonella and
Shigella. Nevertheless, it is now clearly demonstrated that these
indicators have only a limited predictive efficiency when the
contamination is due to viruses or protozoa whose behavior in
the environment is often very different from the behavior of
bacteria in water systems. As a consequence, an important
challenge in modern water microbial quality monitoring is the
rapid, specific, and sensitive detection of reliable microbial
indicators and specific waterborne pathogens.
As the study of interactions between pathogenic
microorganisms and their environment is part of microbial
ecology, this chapter reviews the different types of human
pathogens found in the environment, the different types of
fecal indicators used in water quality monitoring, the biotic
and abiotic factors affecting the survival and the infectivity
of pathogenic microorganisms during their transportation in
the environment, and the methods presently available to
detect rare microorganisms in environmental samples.
This chapter exclusively focuses on human pathogens.
15.2 Different Types of Pathogens
Pathogens in the environment are very diverse: viruses,
bacteria, fungi, protozoa, and cyanobacteria. The main
pathogens of water systems and the diseases they cause are
shown in Table 15.1. We recommend consulting the English
version of the French Institute of Health Surveillance website
(http://www.invs.sante.fr/en) as an example for information
regarding the mandatory reporting of certain diseases. This
site provides a wealth of important information about the
epidemiological surveillance of infections. The reader should
also refer to the following paper on emerging issues in water
and infectious diseases: http://www.who.int/water_sanita
tion_health/emerging/emerging.pdf.
15.2.1 Viruses
A virus is a biological entity that requires a host cell and
its constituents to multiply. It consists of nucleic acid (DNA
or RNA) surrounded by a protein coat called capsid*.
Viruses are obligate parasites* of living cells, either
prokaryotic or eukaryotic. They are able to quickly adapt
to changes in their host and to select processes to bypass the
defenses of the host. Frequent mutations make defenses
against viruses very difficult to implement. They do not
require nutrients to survive, and they can potentially persist
in the environment for long periods of time (weeks to
months). Their size is very small (mostly between 10 and
200 nm). If the virus can infect bacteria, animals, plants, and
humans, we will only focus on human viruses. There are a
wide variety of viruses in the environment that are likely to
cause disease in humans, some of which may have a virus of
animal origin such as avian influenza.
Modern means of communication allow epidemics to propagate at a speed hitherto unparalleled. New viruses and bacteria are identified daily, and at the same time ancient and almost
forgotten diseases such as cholera, avian flu, or others are back
to the actuality. Scientists believe that the twenty-first century
will be that of viruses, and many researchers around the world
are trying to develop methods for the detection, prediction, and
monitoring to address this growing concern.
There are a variety of viruses that cause disease in humans
with more than 150 types of viruses that infect the intestinal
620
P. Lebaron et al.
A large majority of microorganisms are completely harmless
and play essential functions in ecosystems as well as in
human life sustaining. Nevertheless, some microorganisms,
called pathogens*, can cause diseases of varying severity
in humans and animals. Human pathogens are relatively
diverse, belonging to viruses, bacteria, fungi, protozoa, and
algae. They may be present in many different environments
such as water, soil, gastrointestinal tract, and air. The contamination of water by pathogenic microorganisms arguably
represents one of the most significant risks for human health
on a global scale, and there have been numerous cases of
poisoning and disease outbreaks throughout history resulting
directly of poorly treated or untreated water. Water-related
diseases are a major cause of morbidity and mortality worldwide, and contamination of drinking water remains a significant problem, even in OECD countries. Improving the
quality of drinking water is a major public health concern
for the twenty-first century. Moreover, monitoring of drinking water quality is part of a broad control of the microbiological quality of water systems, including groundwater
and surface water (freshwaters and marine waters), which
are increasingly used as drinking water supply. If the health
problems associated with direct consumption of poor water
quality are by far the most important concerns, it is also
important to consider the quality of surface waters used for
irrigation of agricultural lands, aquaculture, and recreation.
The availability of reliable, easy to use, and effective
methods is crucial to ensure the microbiological safety of
water. Whatever the method used, cultivation or direct observation, the great variety of pathogenic microorganisms does not
allow the search for all pathogens and requires the use of “pollution indicators” such as fecal bacteria (e.g., Escherichia coli and
enterococci). Moreover, culture-based methods are timeconsuming, and when they are used to enumerate indicators or
pathogenic bacteria, the time required to obtain a diagnostic is
often too long to protect people from contamination. As an
example, at least 4–5 days are required to diagnose the presence
of Salmonella spp. or Legionella spp. in water samples by
culture processes. The use of the fecal bacteria indicators has
been very helpful in reducing cases of cholera and typhoid and
to protect against pathogenic bacteria such as Salmonella and
Shigella. Nevertheless, it is now clearly demonstrated that these
indicators have only a limited predictive efficiency when the
contamination is due to viruses or protozoa whose behavior in
the environment is often very different from the behavior of
bacteria in water systems. As a consequence, an important
challenge in modern water microbial quality monitoring is the
rapid, specific, and sensitive detection of reliable microbial
indicators and specific waterborne pathogens.
As the study of interactions between pathogenic
microorganisms and their environment is part of microbial
ecology, this chapter reviews the different types of human
pathogens found in the environment, the different types of
fecal indicators used in water quality monitoring, the biotic
and abiotic factors affecting the survival and the infectivity
of pathogenic microorganisms during their transportation in
the environment, and the methods presently available to
detect rare microorganisms in environmental samples.
This chapter exclusively focuses on human pathogens.
15.2 Different Types of Pathogens
Pathogens in the environment are very diverse: viruses,
bacteria, fungi, protozoa, and cyanobacteria. The main
pathogens of water systems and the diseases they cause are
shown in Table 15.1. We recommend consulting the English
version of the French Institute of Health Surveillance website
(http://www.invs.sante.fr/en) as an example for information
regarding the mandatory reporting of certain diseases. This
site provides a wealth of important information about the
epidemiological surveillance of infections. The reader should
also refer to the following paper on emerging issues in water
and infectious diseases: http://www.who.int/water_sanita
tion_health/emerging/emerging.pdf.
15.2.1 Viruses
A virus is a biological entity that requires a host cell and
its constituents to multiply. It consists of nucleic acid (DNA
or RNA) surrounded by a protein coat called capsid*.
Viruses are obligate parasites* of living cells, either
prokaryotic or eukaryotic. They are able to quickly adapt
to changes in their host and to select processes to bypass the
defenses of the host. Frequent mutations make defenses
against viruses very difficult to implement. They do not
require nutrients to survive, and they can potentially persist
in the environment for long periods of time (weeks to
months). Their size is very small (mostly between 10 and
200 nm). If the virus can infect bacteria, animals, plants, and
humans, we will only focus on human viruses. There are a
wide variety of viruses in the environment that are likely to
cause disease in humans, some of which may have a virus of
animal origin such as avian influenza.
Modern means of communication allow epidemics to propagate at a speed hitherto unparalleled. New viruses and bacteria are identified daily, and at the same time ancient and almost
forgotten diseases such as cholera, avian flu, or others are back
to the actuality. Scientists believe that the twenty-first century
will be that of viruses, and many researchers around the world
are trying to develop methods for the detection, prediction, and
monitoring to address this growing concern.
There are a variety of viruses that cause disease in humans
with more than 150 types of viruses that infect the intestinal
620
P. Lebaron et al.