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A comprehensive literature review identifies 1415 species of infectious organism known to be pathogenic to humans, including 217 viruses and prions, 538 bacteria and rickettsia, 307 fungi, 66 protozoa and 287 helminths. Out of these, 868 (61%) are zoonotic, that is, they can be transmitted between humans and animals, and 175 pathogenic species are associated with diseases considered to be 'emerging'. We test the hypothesis that zoonotic pathogens are more likely to be associated with emerging diseases than non-emerging ones. Out of the emerging pathogens, 132 (75%) are zoonotic, and overall, zoonotic pathogens are twice as likely to be associated with emerging diseases than non-zoonotic pathogens. However, the result varies among taxa, with protozoa and viruses particularly likely to emerge, and helminths particularly unlikely to do so, irrespective of their zoonotic status. No association between transmission route and emergence was found. This study represents the first quantitative analysis identifying risk factors for human disease emergence.
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Risk factors for human disease emergence
Louise H. Taylor*, Sophia M. Latham{and Mark E. J. Woolhouse
Centre for TropicalVeterinary Medicine, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG, UK
A comprehensive literature review identi¢es 1415 species of infectious organism known to be pathogenic to
humans, including 217 viruses and prions, 538 bacteria and rickettsia, 307 fungi, 66 protozoa and 287
helminths. Out of these, 868 (61%) are zoonotic, that is, they can be transmitted between humans and
animals, and 175 pathogenic species are associated with diseases considered to be `emerging'. We test the
hypothesis that zoonotic pathogens are more likely to be associated with emerging diseases than non-
emerging ones. Out of the emerging pathogens, 132 (75%) are zoonotic, and overall, zoonotic pathogens
are twice as likely to be associated with emerging diseases than non-zoonotic pathogens. However, the
result varies among taxa, with protozoa and viruses particularly likely to emerge, and helminths
particularly unlikely to do so, irrespective of their zoonotic status. No association between transmission
route and emergence was found. This study represents the ¢rst quantitative analysis identifying risk
factors for human disease emergence.
Keywords: emerging diseases; zoonoses; epidemiology; public health; risk factors
Infectious diseases account for 29 out of the 96 major
causes of human morbidity and mortality listed by the
World Health Organization and theWorld Bank (Murray
& Lopez 1996) and 25% of global deaths (over 14 million
deaths annually) (WHO 2000). The publication of
Emerging infections: microbial threats to health in the United States
by the Institute of Medicine in 1992 (Institute of Medicine
1992) highlighted the fact that numbers of cases of many
infectious diseases, e.g. tuberculosis, cholera and acquired
immune de¢ciency syndrome, are currently increasing
and, over the last few years, there has been a great deal of
discussion of the reasons underlying the `emergence' of
these diseases (e.g. Satcher 1995; Ebel & Spielman 1997;
Greenwood & de Cock 1998; Scheld et al.1998a,b; Binder
et al. 1999). It has been noted (Institute of Medicine 1992;
Morse 1995; Murphy 1998; Palmer et al.1998)thatmany
emerging diseases are zoonoses, infectious diseases which
are transmitted between humans and animals. Emerging
zoonoses include new variant Creutzfeldt^Jakob disease
(The Lancet 1999; Will et al. 1999) and Escherichia coli O157
(Featherstone 1997; Veterinary Record 1997) in Britain, in£u-
enza A strains H5N1and H9N2 in Hong Kong (de Jong et
al. 1997; CDC Press Release 1999), Hantaviruses in the
USA (Schmaljohn & Hjelle 1997) and human sleeping
sickness across Africa (Barrett 1999). These and other
issues, such as the possibility of infections associated with
xenotransplantation (Murphy 1996; Stoye 1998), have
increased concern about the impact of animal pathogens
on human health. However, most studies of disease emer-
gence have been essentially descriptive and more formal
analysis has been hampered by the absence of quantitative
Here, we seek to identify aspects of the epidemiology
of pathogenic species that are associated with increased
risk of disease emergence in humans. Of particular
interest is the hypothesis that zoonotic pathogens are
especially likely to be associated with emerging diseases,
which has not previously been formally tested. We carry
out such a test using the published literature to compile
a list of organisms known to be pathogenic to humans,
together with available information on whether they are
zoonotic, whether they are regarded as emerging, and
on their transmission routes and epidemiologies. Our
approach di¡ers from previous surveys (Murray &
Lopez 1996; WHO 1998) as the focus is the species of
pathogen rather than the disease; many diseases, such as
infant diarrhoea, can be caused by many di¡erent patho-
gens. At this stage we consider simply numbers of
species, treating both common and rare pathogens
equally, without reference to the human disease burden
they currently impose.
(a) Species database construction
The database of pathogens infectious to humans was
compiled from texts of human infectious diseases (Ajello & Hay
1998; Ashford & Crewe 1998; Balows & Duerden 1998; Cox
et al. 1998; Gorbach et al. 1998; Hausler & Sussman 1998; Mahy
& Collier 1998), texts of zoonoses (Hubbert 1975; Andrewes &
Walton 1977; Acha & Szyfres 1987; Bell & Palmer 1988; Beran
1994a,b; Palmer et al. 1998), and, so as to include very recently
identi¢ed human pathogens, reviews of the emerging disease
literature (Morse & Schluederberg 1990; Institute of Medicine
1992; CDC 1994; Wilson et al. 1994; Morse 1995; Roizman 1995;
Schrag & Wiener 1995; Wilson 1995; Osburn 1996; WHO 1996,
1997; Henderson 1997; Meslin 1997; Schwartz 1997; Childs et al.
Phil.Trans. R. Soc. Lond. B(2001)356, 983^989 983 &2001 The Royal Society
doi 10.1098/rstb.2001.0888
*Author for correspondence (
{Present address: Division of Infection and Immunity, Institute of
Biomedical and Life Sciences, University of Glasgow, Glasgow
G12 8QQ, UK
1998; Greenwood & de Cock 1998; Gubler 1998; Scheld et al.
1998a,b;Doboset al. 1999; Mackenzie 1999; Cohen 2000; Mahy
& Brown 2000; Meslin et al. 2000; Pollard & Dobson 2000).
Each entry was a separate species known to be infectious and
capable of causing disease in humans under natural transmission
conditions. Although the de¢nition of species is di¤cult for
some infectious organisms, this is the most appropriate level of
classi¢cation for the vast majority of pathogens and avoids
biases that would otherwise be introduced by organisms that
exhibit a large amount of subspeci¢c variation (e.g. some species
of Salmonella and Listeria).
Ectoparasites (e.g. Arthropoda, Hirudinea) were not included
in the database. Natural transmission was taken to include all
routes (e.g. vector-borne, food-borne, accidental laboratory
infections) apart from deliberate experimental infection.
Infectious pathogenic species only known to cause disease in
immunocompromised patients were included. Species for which
only a single case of human disease has been documented were
included, but this information was noted. Additional references
(Soulsby 1982; Greene 1984; Anderson 1992; Quinn 1994;
Radostits et al. 1994; Carter et al. 1995; Roberts & Janovy 1996;
Urquhart et al. 1996; Aiello 1998) were used to provide
additional information about transmission routes and zoonotic
The following information was collected.
(i) Genus and species name of the pathogen. Nomenclature
followed standard references currently available (Bacterial
nomenclature up-to-date (Deutsche Sammlung von Mikroor-
ganismen und Zellkulturen GmbH), Index virum
(International Committee on Taxonomy of Viruses) and
The CABI bioscience database of fungal names (Funindex)(CABI
Bioscience) (see publishers' entries in References for Web
addresses)). To appear in the database a species name must
¢rst have appeared in an up-to-date source text (published
within the last ten years), and second appeared in an up-
to-date nomenclatural reference source, where available
(see above), or appeared in a second up-to-date source
text, or appeared in an ISI Web of Science Citation Index
search of the last 10 years. Where a genus is known to
cause disease in humans, but no species name was given,
the genus name appears in the database once followed by
`sp.'. Diseases caused by prions were grouped according to
the species of host which is the source of infection. For
three species of parasites (Trypanosoma brucei, Strongyloides
fuelleborni and Nanophyetus salmincola) distinct subspecies are
sometimes given species status. For this study, these species
are included only once in order to maintain consistency
across the database.
(ii) Taxonomic division. Five major divisions were recognized:
viruses (including prions), bacteria (including rickettsia),
fungi, protozoa and helminths (cestodes, nematodes,
trematodes and acanthocephalans).
(iii) Transmission routes to humans. Three categories were
distinguished: direct contact (including via wounds, sexual
contact, vertical transmission or by inhalation), indirect
contact (via food or an environmental reservoir), and
vector borne (by biting or mechanical transfer by arthro-
pods). Where an organism could be transmitted by more
than one route, all were included with equal weighting.
Where no transmission route was documented, this infor-
mation was assumed to be unknown. It was also noted if
the species was known to be transmissible between humans
(by any of the routes listed above).
(iv) Whether or not the species is zoonotic. Zoonoses are
de¢ned, following the World Health Organization (WHO
1959; Palmer et al. 1998), as diseases and infections that are
naturally transmitted between vertebrate animals and
man. Species, such as HIV, which recently evolved from
animal pathogens, but are no longer transmitted between
the animals and humans were not regarded as zoonotic.
Given this de¢nition, the main reservoir hosts for zoonotic
organisms could be either animal or human, but for diseases
where animals played only a minor role in the epidemiology
(so called `zooanthroponoses' (WHO 1959; Palmer et al.
1998)) this information was noted. Organisms with
complex life cycles where vertebrate animals are involved as
intermediate hosts, but humans are the only known de¢n-
itive host, were de¢ned as non-zoonotic; this applied to two
species of protozoa and two species of helminths.
(v) Whether or not the species is emerging. Emerging
pathogens are those that have appeared in a human popu-
lation for the ¢rst time, or have occurred previously but
are increasing in incidence or expanding into areas where
they had not previously been reported (WHO 1997),
usually over the last 20 years (Institute of Medicine 1992).
Some de¢nitions of emerging also include recently discov-
ered aetiological agents of already-described diseases.
However, if there was no evidence that such a pathogen
was increasing in incidence, it was not regarded in this
database as emerging.
A second database was constructed from the ¢rst to allow
investigation of the patterns at the level of genus rather than
species. This was intended to make some allowance for the
potential biases introduced by certain species-rich genera, e.g.
Flavivirus. A genus was considered to be zoonotic, and/or emer-
ging, and/or transmissible by a particular route if at least one
species in it had that characteristic. Twenty-one species (all
viruses) have not been assigned to any genus and were excluded
from this database.
(b) Analysis
Taxonomic division, transmission route and zoonotic status
were considered as potential risk factors. Analyses were
performed comparing emerging and non-emerging species by
taxonomic division, transmission route and zoonotic status and
by combinations of these characteristics. The analyses were
performed at both species and genus level. Results were
expressed as relative risks, which measure the multiplicative risk
relative to species lacking the risk factor. It was assumed
throughout that the lists of all pathogens, zoonotic pathogens
and emerging pathogens were complete, hence further statistical
analyses were not appropriate.
A total of 1415 species of infectious agent in 472
di¡erent genera have been reported to cause disease in
humans according to the criteria used here (electronic
Appendix A, available on The Royal Society's Web site).
The number of species in each of the major taxonomic
divisions and their routes of transmission are shown in
¢gure 1a. Overall, 15% are viruses or prions, 38% are
bacteria or rickettsia, 22% are fungi, 5% are protozoa
984 L. H. Taylor and others Risk factors for disease emergence
Phil.Trans. R. Soc. Lond. B(2001)
and 20% are helminths. Three hundred and ¢fty-seven
species are known to be transmitted by more than one
route but, overall, 43% can be transmitted by direct
contact, 52% by indirect contact, 14% by vectors, and
for 16% the transmission route is not known.
Out of these species, 868 (61%) from 313 di¡erent
genera are known to be zoonotic (electronic Appendix A).
The number of zoonotic species in each of the major
taxonomic divisions and their routes of transmission is
shown in ¢gure 1b. Overall, 19% are viruses or prions,
31% are bacteria or rickettsia, 13% are fungi, 5% are
protozoa, and 32% are helminths. Thirty-¢ve per cent of
zoonotic pathogens can be transmitted by direct contact,
61% by indirect contact, 22% by vectors, and for 6% the
transmission route is not known. Only 33% of zoonotic
species are known to be transmissible between humans
and only 3% of all the zoonotic species are considered to
have their main reservoir in human populations; the
remainder have their main reservoir in animal popula-
tions. The clearest patterns are that helminths are
overrepresented among zoonoses and that fungi are
underrepresented. Also, zoonoses are more likely to be
transmitted by indirect contact or by vectors, and are less
likely to be transmitted by direct contact when compared
with all pathogens (¢gure 1).
A total of 175 species of infectious agents from 96
di¡erent genera are associated with emerging diseases
according to the criteria used here (electronic
Appendix A). The number of emerging species in each of
the major taxonomic divisions and their routes of trans-
mission are shown in ¢gure 1c. Overall, 44% of emerging
species are viruses or prions, 30% are bacteria or
rickettsia, 9% are fungi, 11% are protozoa and 6% are
helminths. Some of these pathogens can be transmitted
by more than one route, but overall 53% of emerging
pathogens can be transmitted by direct contact, 47% by
Risk factors for disease emergence L. H.Taylor and others 985
Phil.Trans. R. Soc. Lond. B(2001)
600 all routes
transmission route
direct contact
indirect contact
0viruses bacteria fungi protozoa helminths
number of species
0viruses bacteria fungi protozoa helminths
number of species
0viruses bacteria fungi protozoa helminths
number of species
Figure 1. Numbers of species of infectious agent causing
human disease, by taxonomic division and transmission route
(noting that some species have more than one transmission
route and for some the transmission route is unknown). (a)All
infectious organisms (n1415). (b) Zoonotic organisms
(n868). (c) Emerging organisms (n175).
Table 1. Risk factors for emergence.
((a) E¡ect of taxonomic division, transmission route and
zoonotic status individually. Relative risk for a particular
category is the proportion of species in that category which
are emerging, divided by the proportion of species not in that
category which are emerging. (b) E¡ect of zoonotic status
within taxonomic and transmission route categories. Within
each category, relative risk refers to the proportion of species
emerging among the zoonotic pathogens divided by the
proportion of species emerging among the non-zoonotic
category relative risk
(a) E¡ect of taxonomic division, transmission route
and zoonotic status individually
zoonotic status non-zoonotic 0.52
zoonotic 1.93
taxonomic division viruses 4.33
bacteria 0.71
fungi 0.33
protozoa 2.49
helminths 0.24
transmission routeadirect contact 1.47
indirect contact 0.80
vector borne 2.35
(b) E¡ect of zoonotic status within taxonomic
and transmission route categories
overall all species 1.93
taxonomic division viruses only 0.96
bacteria only 3.79
fungi only 7.14
protozoa only 0.74
helminths only 0.19
transmission routeadirect contact only 2.13
indirect contact only 2.60
vector-borne only 0.97
aExcludes 222 species (53 zoonotic) with unknown transmission
indirect contact, 28% by vectors, and for 6% the
transmission route is not known.
Risk factors for emergence were ¢rst analysed
separately and the relative risks are presented in table 1a.
One hundred and thirty-two emerging pathogen species
(75%) are zoonotic (electronic Appendix A). This is
substantially more than expected if zoonotic and non-
zoonotic species were equally likely to emerge, and
corresponds to a relative risk of 1.93. This result is
retained when the analyses are repeated at the genus
rather than the species level; 78 out of 96 emerging
genera are zoonotic (81%), compared with 235 out of 376
non-emerging genera (62%). This corresponds to a rela-
tive risk of 2.20, similar to that for species, suggesting that
the result is robust. However, di¡erent risks of emergence
are also associated with di¡erent taxonomic divisions;
viruses and protozoa are overrepresented and fungi and
helminths are underrepresented among emerging species
(electronic Appendix A). A higher risk of emergence is
also associated with vector-borne transmission. These
analyses suggest that zoonotic pathogens are more likely
to emerge than non-zoonotic pathogens, but that the
strength of the e¡ect may be a¡ected by pathogen
taxonomy and transmission routes.
Pathogen taxonomy, zoonotic status, and transmission
routes are not independent (¢gure 1). For example,
virtually all helminths are zoonotic and transmitted by
indirect contact and there are very few vector-borne
fungi. To investigate how these di¡erent risk factors
combine to a¡ect the likelihood of pathogen emergence,
two approaches were taken. First, the e¡ect of zoonotic
status within individual taxonomic and transmission
route categories was investigated (table 1b). The e¡ect of
zoonotic status varies markedly among the taxonomic
groups. Zoonotic bacteria and fungi were more than
three times as likely to emerge than non-zoonotic
bacteria and fungi (relative risks of 3.79 and 7.14, respec-
tively). However, the opposite was true for helminths
with zoonotic species far less likely to emerge than non-
zoonotic ones (relative risk of 0.19). For viruses and
protozoa, zoonotic status appears to make little di¡er-
ence to the risk of emergence (relative risks of 0.96 and
0.74, respectively). Zoonotic pathogens show a higher
probability of emerging if they are transmitted by direct
or indirect contact (relative risks of 2.13 and 2.60,
respectively), but among vector-borne pathogens
zoonotic status made virtually no di¡erence (relative risk
of 0.97). Second, all species were divided into categories
based on taxonomic division, transmission route and
zoonotic status (table 2). Categories with less than ten
species were excluded and the rest ranked by the percen-
tage of species emerging. The most striking result is that
viruses and protozoa account for all of the top seven
categories, all with more than 29% of the species emer-
ging. The next strongest pattern was that zoonotic patho-
gens tended to rank above non-zoonotic pathogens,
although zoonotic helminths transmitted by indirect
contact showed a very low proportion of emerging
pathogens (2%). No obvious pattern was seen associated
with route of transmission.
The majority of pathogen species causing disease in
humans are zoonotic (868 species, i.e. 61% of the total;
electronic Appendix A). In agreement with the original
hypothesis, zoonotic species are overall twice as likely to
be associated with emerging diseases than non-zoonotic
species. However, more detailed analysis shows that there
are also very strong e¡ects of taxonomy on the probability
that a pathogen will be classed as emerging. Viruses and
protozoa are especially likely to emerge and helminths
986 L. H. Taylor and others Risk factors for disease emergence
Phil.Trans. R. Soc. Lond. B(2001)
Table 2. Ranking of categories according to the proportion of species associated with emerging diseases.
(Species in the database fell into 26 categories, seven of which were excluded as they contained less than ten species.)
total number
of species
number of
emerging species
proportion of
species emerging
indirect contact zoonotic viruses 37 17 0.459
indirect contact zoonotic protozoa 14 6 0.429
direct contact zoonotic viruses 63 26 0.413
direct contact non-zoonotic protozoa 15 6 0.400
indirect contact non-zoonotic viruses 13 4 0.308
direct contact non-zoonotic viruses 47 14 0.298
vector borne zoonotic viruses 99 29 0.293
vector borne zoonotic bacteria 40 9 0.225
indirect contact zoonotic bacteria 143 31 0.217
vector borne zoonotic protozoa 26 5 0.192
direct contact zoonotic bacteria 130 20 0.154
indirect contact zoonotic fungi 85 11 0.129
direct contact zoonotic fungi 105 13 0.124
vector borne zoonotic helminths 23 2 0.087
direct contact non-zoonotic bacteria 125 7 0.056
indirect contact non-zoonotic bacteria 63 3 0.048
indirect contact non-zoonotic fungi 120 3 0.025
direct contact non-zoonotic fungi 123 3 0.024
indirect contact zoonotic helminths 250 6 0.024
very unlikely to emerge irrespective of their transmission
routes or zoonotic status. Our attempt to identify risk
factors for emergence points strongly towards taxonomic
and zoonotic status e¡ects.
Interpretation of these results is complicated by uneven
distributions of organisms across the taxonomic divisions,
transmission routes and zoonotic status, and non-
independence between these variables. Helminths are
especially likely to be associated with zoonoses: 95% of
helminth species pathogenic to humans are known to be
zoonotic, compared with 76% of viruses and prions, 65%
of protozoa, 50% of bacteria and rickettsia, and just 38%
of fungi. In addition, zoonoses are relatively likely to be
transmitted indirectly (including transmission by inter-
mediate hosts) or by vectors, suggesting that these trans-
mission routes may be associated with lower host
speci¢city (Woolhouse et al. 2001). These two observations
are not independent; for example, almost all helminths
are transmitted by these routes. The observation that the
route of transmission of over 200 human pathogens (both
zoonotic and non-zoonotic) remains unknown emphasizes
the need for improved understanding of the biology of
infectious agents in general.
An additional factor that may be involved in emer-
gence is transmissibility between humans, because the
incidence of new infections can also be highly sensitive to
small changes in transmission rates within a local human
population. Rigorous analysis is precluded by the absence
of data: for 620 species of infectious agents (44%) the
cited references contain no information on whether they
are transmissible between humans. However, for species
where information is available, the pattern is highly
suggestive. Human-to-human transmissibility is a risk
factor for emergence across all pathogens, with a relative
risk of 2.60.
The most important ¢nding reported here is that
emerging pathogens are not a random selection of all
human pathogens. The next challenge is to explain why
some kinds of pathogenösuch as zoonotic viruses and
protozoa transmitted by indirect contact (table 2)öare
likely to emerge while others are not. It must be emphas-
ized that disease emergence is to some extent subjectively
de¢ned and so any analysis is prone to biases in reporting,
recognition and the availability of information, as may be
associated with di¡erent taxa or di¡erent geographical
regions. Indeed it is sometimes suggested that emerging
disease trends at least partly re£ect biases among the
research community. Nonetheless, we anticipate that
pathogen biology also contributes to the likelihood of
emergence, including such factors as genetic diversity,
generation time and existence of a reservoir (whether
zoonotic or environmental).
This study considers the diversity of pathogens
causing disease in humans, and not the public health
burden imposed by these diseases. Although mortality
and morbidity estimates are now available for some
common infectious diseases (Murray et al.1994;Murray
& Lopez 1996), such data cannot always be attributed
to individual species of pathogen and the health burden
for the vast majority of human pathogens remains
completely unquanti¢ed. Moreover, the importance of
zoonoses is often to be found in the origins rather than
the severity of disease outbreaks. While direct trans-
mission from animals is important for some zoonotic
pathogens, such as rabies, Brucella melitensis and
Mycobacterium bovis, for others, such as in£uenza A and
Dengue, transmission from animals is important mainly
in the origin of outbreaks; the majority of humans are
infected by other humans. This argument is well illu-
strated by the HIVs: these viruses emerged into humans
from a primate reservoir, but rapidly evolved and are
no longer regarded as zoonotic. Nonetheless, animal and
human diseases can be closely associated; recent exam-
ples include Rift Valley fever in Kenya and Somalia
(WHO Press Release 1998), Nipah virus in Malaysia
and Singapore (Chua et al. 2000), West Nile virus in the
United States (Lanciotti et al. 1999) and Hendra virus
in Australia (Westbury 2000). The management of these
pathogens poses challenges outside the scope of tradi-
tional medical practice and demands a much closer
collaboration between medical and veterinary
researchers than has tended to occur in the past.
In conclusion, this study is, as far as we are aware, the
¢rst to identify risk factors for human disease emergence.
This type of analysis, which, hopefully, will be re¢ned
and improved in the future, is essential if emerging
diseases are not always to be regarded as a set of indivi-
dual case studies with no underlying general principles.
We are very grateful to Professor R. W. Ashford (Liverpool
School of Tropical Medicine, UK) for access to data on human
parasites prior to publication and to Dr M. K. Laurenson, Dr L.
Matthews and Professor R. W. Ashford for discussions and
comments on the manuscript. Dr C. BÏchen-Osmond (now at
Biosphere 2 centre, Columbia University, USA) provided valu-
able clari¢cation on virus nomenclature and access to data prior
to publication on the Web. Two anonymous referees provided
very helpful comments. L.H.T. holds a UK Wellcome Trust
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... Zoonoses constitute a significant public health issue worldwide because of the close relationship of humans with animals. Approximately 60 % of infectious diseases have origins in zoonotic pathogens [18]. According to the Centers for Disease Control and Prevention, most zoonotic diseases are bacterial (41.4 %), followed by viral (37.7 %), parasitic (18.3 %), fungal (2 %), and prionic (0.8 %), based on surveillance data [19]. ...
... Zoonotic influenza, salmonellosis, West Nile virus, plague, emerging coronaviruses, rabies, brucellosis, and Lyme disease are the major zoonotic diseases of concern in the United States [23]. Zoonoses comprise a large percentage of new and existing diseases in humans [18]. Some diseases, such as HIV, originated as zoonosis, but later mutated into human-only strains. ...
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Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
... Review pustaka sejauh ini telah mengidentifikasi ada 1415 spesies mikroorganisme infeksius yang bersifat patogen (menyebabkan penyakit) pada manusia (Taylor, Latham and Woolhouse, 2001). Dari 1415 jenis mikroorganisme ini, terdapat 217 virus dan partikel kecil (prions), 528 bakteri dan riketsia, 307 jamu, 66 protozoa dan 287 jenis dari cacing. ...
... Sekitar 61 % (868 jenis) adalah hidup di tubuh hewan dan dapat menularkan ke manusia (zoonosis) dan 175 jenis lainnya menyebabkan penyakit-penyakit yang bisa muncul kapan saja (emerging). Dari jumlah tersebut, 132 jenis adalah zoonosis (Taylor, Latham and Woolhouse, 2001). ...
... Depending on the way of transmission, they can be foodborne, waterborne, vector-borne, transmitted through direct contact with animals, or indirectly by fomites or environmental contamination. These diseases represent a severe threat to worldwide public health by now, constituting approximately 60% of all emerging infectious diseases reported globally [1]. For this reason, considerable efforts have recently been made to set up integrated surveillance plans [2], [3] paving the way towards early recognition and intervention of critical settings. ...
... C. Ippoliti, F. Iapaolo, and A. Conte are with Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G.Caporale', Teramo, Italy. 1 This work has been submitted to the IEEE Transactions On Geoscience And Remote Sensing for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. ...
The occurrence of West Nile Virus (WNV) represents one of the most common mosquito-borne zoonosis viral infections. Its circulation is usually associated with climatic and environmental conditions suitable for vector proliferation and virus replication. On top of that, several statistical models have been developed to shape and forecast WNV circulation: in particular, the recent massive availability of Earth Observation (EO) data, coupled with the continuous advances in the field of Artificial Intelligence, offer valuable opportunities. In this paper, we seek to predict WNV circulation by feeding Deep Neural Networks (DNNs) with satellite images, which have been extensively shown to hold environmental and climatic features. Notably, while previous approaches analyze each geographical site independently, we propose a spatial-aware approach that considers also the characteristics of close sites. Specifically, we build upon Graph Neural Networks (GNN) to aggregate features from neighbouring places, and further extend these modules to consider multiple relations, such as the difference in temperature and soil moisture between two sites, as well as the geographical distance. Moreover, we inject time-related information directly into the model to take into account the seasonality of virus spread. We design an experimental setting that combines satellite images - from Landsat and Sentinel missions - with ground truth observations of WNV circulation in Italy. We show that our proposed Multi-Adjacency Graph Attention Network (MAGAT) consistently leads to higher performance when paired with an appropriate pre-training stage. Finally, we assess the importance of each component of MAGAT in our ablation studies.
... More than 25% of the annual deaths across the globe is recorded due to such emerging diseases [5,6]. Between more than 50 emerging contagions, around 10% microbial agents have been identified during the most recent 40 years [7,8]. ...
... The ability of these pathogens to infect multiple tissues while undergoing morphogenetic shifts makes fungal diseases differ significantly from other infections (Li and Nielsen 2017). Over 600 fungal pathogens that may cause diseases in humans have been reported so far, and among them, Aspergillus, Candida, Cryptococcus and Pneumocystis species are the most common (Taylor et al. 2001;Morio et al. 2020;Rodrigues and Nosanchuk 2020). Fungal infections in humans or mycoses vary from mild to life-threatening, with various symptoms. ...
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Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of –OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.
... In this context, an important role might have been played by the food system. In fact, many factors, such as direct or indirect contact with animals, especially wild species, or the consumption of their meat, particularly inadequately cooked, could have determined the spillover that leads to the emergence of a new zoonotic disease [12]. For SARS-CoV-2, the first evidence is most likely to be traced back to the Huanan seafood wholesale market (Wuhan, China), a wet market selling both food and live wild animals [13][14][15]. ...
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The SARS-CoV-2 pandemic is being questioned for its possible food transmission, due to several reports of the virus on food, outbreaks developed in food companies, as well as its origins linked to the wet market of Wuhan, China. The purpose of this review is to analyze the scientific evidence gathered so far on the relationship between food and the pandemic, considering all aspects of the food system that can be involved. The collected data indicate that there is no evidence that foods represent a risk for the transmission of SARS-CoV-2. In fact, even if the virus can persist on food surfaces, there are currently no proven cases of infection from food. Moreover, the pandemic showed to have deeply influenced the eating habits of consumers and their purchasing methods, but also to have enhanced food waste and poverty. Another important finding is the role of meat processing plants as suitable environments for the onset of outbreaks. Lessons learned from the pandemic include the correct management of spaces, food hygiene education for both food workers and common people, the enhancement of alternative commercial channels, the reorganization of food activities, in particular wet markets, and intensive farming, following correct hygiene practices. All these outcomes lead to another crucial lesson, which is the importance of the resilience of the food system. These lessons should be assimilated to deal with the present pandemic and possible future emergencies. Future research directions include further investigation of the factors linked to the food system that can favor the emergence of viruses, and of innovative technologies that can reduce viral transmission.
Environmental pathogen reservoirs exist for many globally important diseases and can fuel disease outbreaks, affect pathogen evolution, and increase the threat of host extinction. Differences in pathogen shedding among hosts can create mosaics of infection risk across landscapes by increasing pathogen contamination in high use areas. However, how the environmental reservoir establishes in multi-host communities and the importance of factors like host-specific infection and abundance in environmental contamination and transmission remain important outstanding questions. Here we examine how Pseudogymnoascus destructans , the fungal pathogen that causes white-nose syndrome in bats, invades and establishes in the environment. We quantified dynamic changes in pathogen shedding, infection intensities, host abundance, and the subsequent propagule pressure imposed by each species within the community. We find that the initial establishment of the pathogen reservoir is driven by different species within the community than those that are responsible for maintaining the reservoir over time. Our results also show that highly shedding species do not always contribute the most to pathogen reservoirs. More broadly, we demonstrate how individual host shedding rates scale to influence landscape-level pathogen contamination. Open Research statement Data will be made available through the Dryad Digital Repository before publication or upon reviewer request.
The history of pandemic diseases provides a cautionary tale about the vulnerability of human populations to environmental threats. Many have interpreted our current pandemic as evidence of increasing disruption to natural ecosystems and the havoc this can cause as humans are exposed to new pathogens. An initial focus on a Chinese market as the source of the virus turned attention to human interactions with wildlife, and many hope that the pandemic may provide a turning point if the threat of disease stimulates a renewed interest in the conservation of species and wild places. Additionally, declining air pollution and renewed animal activity in human spaces during lockdown emboldened many to push for further environmental measures to be put in place via a green approach to rebuilding economies. On the other hand, global recession will likely limit funding and willingness to invest in conservation measures, potentially signaling a significant retreat from current environmental efforts. Furthermore, problems with solid waste disposal highlight significant environmental challenges associated with the pandemic. Whether short-term environmental improvements associated with the pandemic can be translated into longer-term environmental gains will prove critical to both environmental and public health futures.KeywordsEcologyEnvironmentPollutionPublic healthWildlife
Most of the new emerging and re-emerging zoonotic virus outbreaks in recent years stem from close interaction with dead or alive infected animals. Since late 2019, the coronavirus disease 2019 (COVID-19) has spread into 221 countries and territories resulting in close to 300 million known infections and 5.4 million deaths in addition to a huge impact on both public health and the world economy. This paper reviews the COVID-19 prevalence in animals, raise concerns about animal welfare and discusses the role of environment in the transmission of COVID-19. Attention is drawn to the One Health concept as it emphasizes the environment in connection with the risk of transmission and establishment of diseases shared between animals and humans. Considering the importance of One Health for an effective response to the dissemination of infections of pandemic character, some unsettled issues with respect to COVID-19 are highlighted.
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Background: Zika virus (ZIKV) was discovered in 1947 with the virus isolation from Rhesus monkey (Macaca mulatta) in Uganda forest, Africa. Old World Primates are involved in a sylvatic cycle of maintenance of this arbovirus, however a limited knowledge about the role of New World primates in ZIKV transmission cycles has been established. Objective: This work aimed to investigate the presence of enzootic circulation of ZIKV in New World Primates from three Brazilian states: São Paulo, Paraíba, and Paraná. Methods: We analyzed 100 non-human primate samples collected in 2018 and 2020 from free-ranging and captive environments from São Paulo (six municipalities belonging to Sorocaba region), Paraíba (João Pessoa municipality), and Paraná (Foz do Iguaçu municipality) using reverse transcriptase quantitative polymerase reaction (RT-qPCR) assays, indirect enzyme-linked immunosorbent assay (ELISA), and plaque reduction neutralization test (PRNT). Findings: All samples (n = 141) tested negative for the presence of ZIKV genome from tissue and blood samples. In addition, all sera (n = 58) from Foz do Iguaçu' non-human primates (NHPs) were negative in serological assays. Main conclusion: No evidence of ZIKV circulation (molecular and serological) was found in neotropical primates. In addition, the absence of antibodies against ZIKV suggests the absence of previous viral exposure of NHPs from Foz do Iguaçu-PR.