Download editorial mining the natural world for new pathogens

Am. J. Trop. Med. Hyg., 67(2), 2002, pp. 133–134
Copyright © 2002 by The American Society of Tropical Medicine and Hygiene
EDITORIAL
MINING THE NATURAL WORLD FOR NEW PATHOGENS
DAVID A. RELMAN
Departments of Microbiology & Immunology, and of Medicine, Stanford University School of Medicine, Stanford, CA 94305, and
Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304
these sequences is unknown. Nonetheless, this study illustrates the power of this generic approach, as well as our incomplete understanding of Bartonella diversity.
Broad range PCR is an effective and commonly-used molecular approach for pathogen discovery7, and is well-suited
for “mining” the natural world. In previous work, the group
from Marseilles has described the results of a search for Rickettsia sequence types in ticks;8 they also reviewed the use of
vector surveillance based on specific pathogen PCR assays for
anticipating disease outbreaks.9 Other potentially promising
sites for molecular mining efforts are insect vectors, such as
mosquitoes and sandflies, fruit bats, water fowl, and a variety
of small rodents—from whom hemorrhagic fever, encephalitis, and respiratory viruses, and Borrelia species, to mention a
few, have been discovered in recent years.
Despite the power of broad range PCR with its relative lack
of bias and its suitability for examining archival or poorly
preserved specimens for uncultivable organisms, it has limitations and problems. First, our ability to infer phenotype,
such as virulence, from genotype alone is imperfect at best.
This limitation is even more acute when only small amounts
of DNA sequence are available from any given organism.
Second, distinguishing and defining operational taxonomic
units from pools of closely related sequences is difficult. As a
result, we might find ourselves addressing clusters of sequence types as single entities. Third, the presence of sequence alone tells us little about the dynamic relationship of
the putative organism with its local environment, or even its
viability; analysis of RNA transcripts and in situ methods of
localizing genetic material might partially alleviate this problem. Finally, PCR using broad range primers for a group of
related sequence targets may be less sensitive than a PCR
using specific primers for any single unique target belonging
to the group.
Given these limitations, how should one proceed with investigating a potential PCR “hit” within a suspect microbial
vector or reservoir? There are a number of possible avenues,
including acquisition of additional genome sequence, physicoanatomic localization of the sequence, assessment of in situ
gene expression, and efforts to cultivate the putative pathogen. In general, the stronger the association of the detected
sequence with temporally or geographically linked human
disease, the easier it might be to justify a vigorous and comprehensive investigation. In the absence of a cultivated organism and an appropriate disease model, there are alternative criteria for evaluating a possible causal link with disease.10 Clearly, these lines of investigation can be laborious.
Regardless of how extensively a lead is pursued, efforts to perform microbial surveys of nature and mine likely sites for pathogens should be encouraged. Experience has taught that the rewards of these sorts of data are often not realized until later.
Surveys of the natural world reveal a staggering number of
previously unrecognized and uncharacterized microbial life
forms. When molecular detection methods are used, in most
environmental sites at least 100-fold greater prokaryotic diversity is discovered than has been detected using cultivationbased methods.1 Nearly all of these environmental microorganisms persist in an equilibrium state with their local environment, and are not believed or expected to be virulent for
humans. This apparent lack of virulence reflects a combination of two factors: inadequate “means” and insufficient “opportunity”. Some environmental microbes are not suited for,
or adapted to growth in humans; they lack the genetic features (means) for virulence. On the other hand, there is a
small subset of microbes and viruses on this planet that have
not yet been recognized as disease-causing agents, but would
be capable of causing human disease if provided adequate
contact with humans. A variety of behavioral, political, climatic, and host biologic factors can create these opportunities. For example, hantavirus pulmonary syndrome appeared
in the U.S. Southwest when a desert mouse population, rapidly expanding as a consequence of long-awaited rain, and
starving because of a food supply inadequate to meet its
needs, fled to human settlements in the region. They were
carrying Sin Nombre virus and shedding it in and near the
homes of susceptible new hosts. Bartonella henselae was not
recognized until it found a suitable population of immunocompromised humans in whom it could cause dramatic pathology (bacillary angiomatosis), and until adequate detection methods, both cultivation-based and molecular, had been
developed.2 Without a significant epidemiologic or clinical
event to prompt closer attention, these occult pathogens
would remain an unobtrusive feature of the natural world.
Studies of emerging infectious diseases suggest that newlyrecognized pathogens are often established in vectors and
reservoirs within the local environment well before they are
discovered as human pathogens.3,4,5 One might argue that by
deliberately scrutinizing these vectors and reservoirs using the
appropriate methods, we might be afforded early warning
about potential disease-causing agents. At the least, these surveys would expand our appreciation of microbial diversity
and inferred microbial function.
Parola and colleagues have addressed this need by examining known arthropod vectors of disease for a family of enigmatic bacterial symbionts and pathogens.6 Using a broad
range PCR approach, they examined fleas, lice, and ticks in
Peru for the possible presence of members of the genus Bartonella. Four of 98 arthropod specimens contained Bartonella
DNA. The four Bartonella DNA sequences represented
novel genotypes; three appeared to be significantly different
from previously characterized Bartonella species. The clinical
significance of the organisms whose existence is inferred from
133
134
RELMAN
Author’s address: Veterans Affairs Palo Alto Health Care System
154T, Building 101, Room B4-185, 3801 Miranda Avenue, Palo Alto,
CA 94304, E-mail: [email protected], Phone: (650) 852-3308, Fax:
(650) 852-3291
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