Mapping Bacterial Genomes:
into Infectious Disease-Causing Agents
A. Reynolds, MSPH, Ph.D.
Human Genome Project website
Recently, you've most likely heard
about the human genome project in the media- science's international
effort focused on mapping the entire human genome.1 Knowledge of organizing human genetic building
blocks promises to provide needed information on the basic structure
and function of the body while enabling researchers to target areas
of disease origin, diagnostics, treatment and therapy. Did you know
the same technology is also being applied to waterborne pathogens?
Researchers have now determined the complete genomic sequence of
the agent responsible for choleraa potentially fatal waterborne
disease striking in epidemic proportions worldwide.
Genome sequencing has increased in popularity in recent years with
the advent of new molecular methodologies that enable scientists
to determine the basic genetic make-up of just about any organism-from
bacteria to humans. Once the genetic building blocks are mapped,
one can begin to evaluate possible evolution of the organism and
its relation to other species-location of genes that code for fatal
or debilitating diseases (i.e., cancer genes) or traits that enable
increased survival and persistence (i.e., antibiotic and chlorine
In the case of many
bacteria, a variety of strains exist. Some, or even the majority,
aren't harmful. A good example is the bacterium, E. coli.
For decades, all strains of this organism were considered harmless
indicators of fecal contamination, indicative of the possible presence
of other pathogens also found in feces. Interest in this organism
has peaked since several virulent strains have been associated with
both food and water outbreaks (i.e., strain O157:H7) resulting in
numerous fatalities, primarily in children and the elderly-most
notably in Walkerton, Ontario, in May and a county fair in upstate
New York last summer.
In light of the emergence
of new pathogens and increased bacterial resistance to antibiotics,
genetic sequencing tools provide new information on the life of
a pathogenic organism that may aid in development of new antibiotics
and vaccines. Sequence data also provides new ways of looking at
the evolutionary history of bacteria. Unfortunately, whole genome
sequencing is a daunting task. Led by Dr. Frederick R. Blattner
of the University of Wisconsin in Madison, the genetic mapping of
one strain of E. coli took nearly six years and the collective
efforts of more than 250 scientists.2
Genetic analysis of
the pathogenic region of the E. coli showed related sequences
to Shigella, a known pathogen. Portions of the pathogenic
Shigella organism may have integrated with the harmless E.
coli to create a new pathogen. We know that organisms in the
environment can "share" genetic information and this sharing
of genes may enable a new pathogen to emerge or become particularly
resistant to treatment. Understanding, through molecular characterization
studies, how these genes are transferred-and at what frequency-will
enable researchers to better develop strategies for preventing the
emergence or transmission of these pathogens. Only a handful of
bacteria have been entirely sequenced, but the trend is increasing.
Recently, Vibrio cholerae has been added to the list of organisms
for which the complete genomic sequence is available.3 The complete sequence was determined from a representative
isolate of the ongoing seventh pandemic of cholera in Asia. The
V. cholerae genome is composed of more than four million
DNA base pairs, requiring the expertise of more than 30 researchers
to fully sequence. The organism has a diverse natural habitat, can
be attached to zooplankton, exists in the water column in a free-floating
state and may also act as a human pathogen in the gastrointestinal
tract. Genetic mapping of V. cholerae revealed areas coding
for several pathogenic factors including toxin production and intestinal
colonization. Evaluation of the sequence information may aid researchers
in determining how a commonly found, free-living marine organism
can also act as a human pathogen.
The cholera pandemic
Hundreds of thousands of people are sickened by V. cholerae
throughout the world. In 1999 alone, 220,000 cases were reported
resulting in more than 8,400 deaths. The current seventh pandemic
began in 1961 in Indonesia. The disease rapidly spread to Asia and
Bangladesh in 1963. By 1966, the epidemic reached India, the former
Soviet Union, Iran and Iraq. Cases occurred in Africa in 1970, after
an absence of over 100 years of the disease.
Peru was struck in
1991 and the disease has spread throughout South America. The epidemic
in Latin America is proving to be difficult to contain due to the
lack of modern infrastructure, water and wastewater treatment methods
and a safe, clean supply of drinking water. In addition, since coastal
waters are natural reservoirs for the organism, it's unlikely that
exposures to the pathogen itself will ever be eliminated. The number
of countries currently affected approaches 120 and continues to
increase. From 1997 to 1998, there was a surge of cholera cases,
with the total number nearly doubling. The disease is rare in the
United States (0-5 cases per year) or in countries where sanitation
is good and water supplies are pure or treated.
Cholera is transmitted
by contaminated food or water. The organism may be present in feces
or vomit of infected individuals. Thus, contamination events may
be direct from the natural environment or indirect from the feces
of an infected individual. Even those unaware that they're infected
may continue to propagate spread of the disease since the organism
may be found in feces for 7-to-14 days after infection. The disease
tends to spread rapidly in areas with poor sanitation. The bacterium
survives well in brackish and marine waters and outbreaks have been
associated from raw or undercooked shellfish.
are often mild or produce no symptoms at all; however, approximately
one in 20 persons suffers severe symptoms involving profuse watery
diarrhea, vomiting and leg cramps. If treatment isn't issued immediately,
death can result within 24 hours, killing up to 50 percent of those
infected. Treatment for cholera involves rehydration with oral rehydration
solution or intravenously. Antibiotics may increase recovery time
but isn't necessary for successful treatment. Vaccines are currently
available for V. cholerae but are only effective 50 percent
of the time and, at best, last only six months.
V. cholerae can
survive in a variety of foods for up to five days at room temperature
and longer when refrigerated. Freezing prevents proliferation of
the organism but doesn't kill it. The organism is however sensitive
to acid environments (i.e., carbonated beverages) and drying. Cholera
infections may be avoided by drinking only treated water and ice
(i.e., boiled, chlorine, iodine, reverse osmosis, etc.), and cooking
foods thoroughly. Raw vegetables should be peeled and raw or undercooked
seafood should be avoided as should foods and beverages from street
vendors. The World Health Organization offers this simple rule:
"boil it, cook it, peel it, or forget it."
Like E. coli,
V. cholerae includes both pathogenic and nonpathogenic strains
that can be differentiated by examination of their genetic maps.
Certain strains are also severe pathogens for fish and mammals.
They're indigenous inhabitants of marine environments, whose presence
doesn't necessarily indicate a contamination event. An important
trait of the organism is that it's able to enter a viable but nonculturable
state under certain environmental conditions and thus becomes undetectable
by conventional cultural methods, while still capable of initiating
disease. Evaluation of genetic differences amongst strains may provide
further clues as to the physiological changes and the emergence
and survival of this puzzling organism.
The aim of genetic sequencing is to understand the evolution and
basis of pathogenicity and environmental persistence of various
organisms. In addition, how organisms exchange information and to
what end they can emerge as new pathogens is of interest. Finally,
new vaccines and medicines may be developed that can better address
the prevention of epidemic infections of V. cholerae. Complete
genome sequencing may at first initiate more questions than answers.
Although the enormous task of sequencing the organism is done, it's
only a starting point for countless other research endeavors. An
understanding of what the genomic traits infer shall remain topics
of further investigation for decades to come.
Currently, the University of Wisconsin Genome Project lists approximately
five more pathogenic E. coli strains that are being sequenced
in their entirety in addition to a strain of Shigella flexneri
(cause of dysentery), Salmonella typhi (cause of typhoid
fever) and Yersenia pestis (cause of plague).4 As information unfolds regarding the implications
of the human genome map, molecular technologies promise to continue
to reveal new insights into waterborne bacteria and other pathogenic
organisms and how they relate to human health.
Genome Project Information, Oak Ridge National Laboratory, Oak Ridge,
2. Blattner, F.R., et al., "The complete genome sequence of
Escherichia coli K-12," Science, 277(5331)1453,
3. Heidelberg, J.F., et al., "DNA sequence of both chromosomes
of the cholera pathogen Vibrio cholerae," Nature
406, 477-483, 2000.
4. University of Wisconsin Genome Project home page: www.genomewisc.edu