Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.
Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.
OCR for page 193
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line Appendix K Interactions of Infectious Agents with the Host PLANT PATHOGENS Examples are given by the major evolutionary mechanisms by which plant pathogens have emerged as threats to agricultural ecosystems. These mechanisms take place over variable time scales ranging from short to hundreds or thousands of years. Host-Tracking Host-tracking refers to a co-evolution of a pathogen with its host during the process of host domestication, which includes the formation of a specific agro-ecological system. Host-tracking includes the selection and cultivation of desirable host genotypes, processes that simultaneously select for pathogen genotypes adapted to the selected individuals and the agro-ecological conditions in which the process occurred. The process can take seven to twelve thousand years and pathogen and host share the same center of origin. A documented example is Mycosphaerella graminicola on wheat, (Stukenbrock, Banke et al. 2007). The emergence of this pathogen causing the Septoria tritici leaf blotch disease on wheat was studied by genealogical and model-based coalescent approaches on seven selected genes from 184 isolates (Stukenbrock, Banke et al. 2007). Two related but genetically differentiated wild grass-infecting populations of M. graminicola named S1 and S2, and adapted to wheat, were identified on wild grasses collected in northwest Iran. The S1 and S2 populations were encountered on three different weedy grass species growing in the proximity of fields cultivated with wheat. The analysis indicated that the split between the most closely related wild grass infecting population S1 and M. graminicola occurred approximately 10,000 to 12,000 years ago, which coincides with the time
OCR for page 194
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line that wheat was domesticated, suggesting a co-speciation of the host and pathogen. Similarly, another fungal pathogen Magnaporte oryzae, the causal agent of rice blast disease, underwent a host speciation due to the loss of the avirulence gene AVR-Co39 that was frequent in haplotypes from other hosts. The genetic isolation and divergence of an epidemic lineage from other populations on grasses may have resulted from rapid clonal propagation and strong selection mediated by the new domesticated host and its associated agro-ecosystem. The subsequent intensification and dissemination of this crop favored the propagation and global dispersal of clones of the rice-infecting blast pathogen (Couch, Fudal et al. 2005). Host Shift Host shift is a process in which a new pathogen emerges by adaptation to a new host that is a close relative of the former host (e.g., shifting from a wild crop to the new domesticated selection or variety of the crop). The process takes from less than 500 to 7,000 years, and the pathogen and host do not always originate in the same center of origin (Stukenbrock and McDonald 2008). An example is the shift of Rhynchosporium secalis from wild grasses to barley and rye. This was an abrupt evolutionary change that took approximately 2,500-5,000 years, much later than the domestication of barley and rye. R. secalis causes scald diseases and infects barley (Hordeum vulgare), rye (Secale cereale), and other grasses. A RFLP allelic diversity analysis of 1,366 geographical isolates indicated that the center of diversity of this pathogen did not coincide with the center of origin of barley, similar to the pattern found for the avirulence gene NIP1 (O.24). NIP1 has a dual function as both an elicitor of plant defense and as a toxin-encoding gene (O.25). NIP1 is often deleted (O.26) because its role as elicitor for plant defense drives this gene under positive diversifying selection. Further analysis of R. secalis revealed phylogenetic relationships between different host-related lineages (O.27). These analyses confirmed a later emergence of the scald pathogen, most likely between 1,200-3,600 years after the introduction of the barley agro-ecosystem into northern Europe. Host Jump Host jump describes a process through which a new pathogen emerges in a host species that is genetically distant from the original plant host (e.g., from another class or order). In this case, the geographical origin of the host does not always correspond with the geographical origin of the pathogen as observed in the host shift process. An example is the emergence of Magnaporthe oryzae, which also fits into a host-tracking co-evolutionary scenario with rice; however, the emergence of a rice-infecting lineage also involved a number of host shifts from Setaria millet to rice (Couch, Fudal et al. 2005). The close proximity
OCR for page 195
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line between crop plants can facilitate a host jump of pathogens associated with either one of the species. We will consider the evolutionary relationship between M. oryzae haplotypes on rice and on weeds of rice. The more ancestral haplo-types originated from rice, whereas haplotypes from weeds of rice were found at the tips of a haplotype network. After additional host jumps that occurred to common weeds of rice, including cutgrass (Leersia hexandra) and torpedo grass (Panicum repens), the host specialization of the rice-infecting lineage occurred (Couch, Fudal et al. 2005). HOST SPECIES TROPISM Variola and Monkeypox Viruses What we know concerning variola and monkeypox virus virulence genes involved in host species tropism comes by analogy to well-characterized orthopoxvirus orthologues. Different poxviruses encode a different pattern of virulence genes that is the basis for their unique host biology. The function of a large number of these virulence genes is to ensure the infected cell or neighboring cells are metabolically active and capable of efficient production of progeny virus. Virulence genes encoded by monkeypox and variola viruses are listed for convenience as targeting five pathways: inhibitors of apoptosis, an early cellular protective response that eliminates virus-infected cells and limits virus replication; inhibitors of pathogen recognition receptor (PRR) pathways that are triggered by pathogen associated molecular patterns (PAMPs) such as dsRNA and DNA; inhibitors of the interferon response, which induces a large number of unique antiviral molecules; modulators of the ubiquitin ligase system that regulates a large number of intracellular processes modulators of cell cycle and processes associated with transcription, DNA replication, and protein synthesis. Genome comparisons identified 12 virulence genes that differed between variola and monkeypox viruses. The majority of these genes affect cell processes (i.e., apoptosis blockers, 2 genes and PRR and IFN responses, 7 genes). These differences are hypothesized to explain the dramatic difference in the animal species that act as reservoir or incidental hosts for the viruses. Monkeypox virus has a broad host range and several animal species may act as reservoir hosts in nature. In addition, field studies conducted in the lowland tropical forests of the Congo Basin and West Africa revealed that monkeypox virus can infect many animal species, including squirrels (Funisciurius spp. and Heliosciurus spp.)
OCR for page 196
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line and non-human primates (such as Cercopithecus spp.; Parker S). Variola virus, on the other hand, has human as the sole reservoir species and fails to cause experimental disease in standard adult, small animal, and non-human primate models under physiological conditions. Franciscella Tularensis Tularemia is a zoonotic disease caused by one of several subspecies of Francisella tularensis. F. tularensis subsp tularensis and subsp holarctica are most commonly associated with disease in humans. Outbreaks of disease in humans commonly occur during disease cycles in rodents and lagomorphs, mostly as a result of transmission from one mammal to another by one of a number of arthropod vectors. F. tularensis is a facultative intracellular bacterium that can infect humans via the skin (ulceroglandular), the conjunctiva (oculoglandular), the mouth (oropharyngeal or gastrointestinal), or the airway (pneumonic). Macrophages are the primary target cell for F. tularensis, which is taken up by asymmetric pseudopod loops formed by the macrophage in a complement-dependent manner. Intracellular survival of F. tularensis is a complicated process that involves, but is likely not limited to, genes encoded on the large Francisella pathogenicity island. Genomic and proteomic analysis of F. tularensis spp. identified a large number of hypothetical genes/proteins with no homology to known genes and proteins. Thus, F. tularensis spp. provide ideal examples of organisms for which knowledge of genomic sequence does not allow for prediction of virulence. Rickettsia Species The Rickettsia genus contains at least 18 species, all of which are flea- or tick-borne bacteria (Gillespie, Ammerman et al. 2009). R. prowazekii and R. typhi are the etiological agents of typhus and murine typhus, respectively, and R. rickettsii is the causative agent of Rocky Mountain Spotted Fever. R. prowazekii is transmitted from louse to mammalian host in the feces of the louse; the rickettsia are deposited onto the host skin by the louse and subsequently enter the bloodstream of the host via scarification of bites. Naïve lice become infected through feeding of the mammalian host, thus renewing the life cycle of the rickettsia. R. typhi are transmitted to rodents, primarily rats, by a similar mechanism except that the arthropod vector is the flea. An uncommon sequela to typhus is the development of a recrudescent illness, known as Brill-Zinsser disease, during which R. prowazekii can sequester itself within the host for months to years. Because infection of a mammalian host results from death of the louse, Brill-Zinsser disease may represent a mechanism by which R. prowazekii can be maintained and transmitted for many years following the initial infection. R. rickettsii, on the other hand, is transmitted to its mammalian host
OCR for page 197
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line through the bite of a tick; the tick can infect multiple hosts because it does not die as a result of the R. rickettsii infection. Little information is available about the rickettsial genes that are required for entry into and replication within the arthropod vector of any of the known Rickettsia species. The genomes of the typhus-causing rickettsia and R. felis (another insect-borne Rickettsia species) are surprisingly different given that they share similar arthropod hosts and cause similar diseases (of varying intensity) in their mammalian hosts. Of note, only two open reading frames are shared specifically by the insect-borne Rickettsia species (R. prowazekii, R. typhi, and R. felis); these genes are linked on the chromosome and are thought to have been acquired by lateral gene transfer, which is a newly discovered phenomenon in the rickettsial species (Gillespie, Ammerman et al. 2009). However, the function of the open reading frames is unknown. Thus, once again, knowledge of the genome sequence of a group of related organisms does not allow us to predict the pathogenicity of any of the organisms. HOST INNATE RESPONSES AND PATHOGEN-ENCODED COUNTERMEASURES Microbial pathogens have evolved complex and efficient methods to overcome both innate and adaptive immune host responses to infection. Here we provide a few examples from the large number of the diverse approaches that viruses and bacteria have evolved to evade and subvert key, innate antimicrobial responses in animals and plants. Plant Innate Defense System Plants have evolved resistance (R) genes encoding proteins that confer resistance to specific pathogens. The plant pathogen molecule that specifically elicits R-protein-mediated responses is termed an avirulence (Avr) determinant. The Avr proteins are usually necessary for successful infections and are virulence factors in a susceptible host (Soosaar, Burch-Smith et al. 2005). For example, the Arabidopsis thaliana RCY1 gene confers resistance to the Y strain of Cucumber mosaic virus (CMV), but not to the O strain. When the Y strain of CMV infects RCY1-containing plants, a defense response that restricts the virus to the infection site and prevents disease is initiated. The virus is an avirulent pathogen on these resistant plants and this is termed an incompatible interaction (Soosaar, Burch-Smith et al. 2005). A. thaliana encodes a second R gene, HRT, which confers a hypersensitive response (HR) to Turnip crinkle virus (TCV). Both RCY1 and HRT genes are allelic and encode proteins that share 91 percent similarity but confer resistance to unrelated viruses: CMV, a cucumovirus and TCV, a carmovirus, respectively. Another example in Nicotiana glutinosa is the N gene which confers resistance to Tobacco mosaic virus (TMV, a Tobamovirus) (Soosaar,
OCR for page 198
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line Burch-Smith et al. 2005; Bent and Mackey 2007). In order to establish a rapid and productive infection, a plant virus must enter the plant cell with defense proteins or immediately synthesize them. Examples include the following: The P1-HcPro encoded by Turnip mosaic virus (TuMV), a virus with a RNA genome, interferes with the miRNA-controlled development pathways that share components with the antiviral RNA-silencing pathway. This interference acts as a viral counter-defense mechanism that enables systemic infection by TuMV (Dunoyer, Lecellier et al. 2004); The p19 proteins from a number of tombusviruses including Tomato bushy stunt virus, Cymbidium ringspot virus, and Carnation Italian ringspot virus allow a high accumulation of viral RNAs and also are responsible for TBSV pathogenesis (Qiu, Park et al. 2007). The CP (capsid protein), p20, and p23 proteins of Citrus tristeza virus each have an unique suppressor of RNA silencing activity (Lu, Folimonov et al. 2004). The 2b protein encoded by CMV performs as a suppressor of RNA silencing and a pathogenicity determinant (Anandalakshmi, Pruss et al. 1998; Brigneti, Voinnet et al. 1998). The p25 of Potato virus X which blocks the host silencing signal from spreading to other cells (Voinnet, Lederer et al. 2000). Pseudomonas syringae AvrPto and AvrPtoB act upstream of the MAP kinase signaling to suppress transcription of a few transcripts induced by flagellin via PRR FLS2. Other bacteria with avirulence genes are: Pseudomonas syringae pv. glycinea (avrA, avrB and avrC); Pseudomonas syringae pv. Tomato (avrD, avrRpt2, and avrPto); Xanthomona campestris pv. Vesicatoria (avrBs1, avrBs2); and Xanthomonas campestris pv. raphani (avrXca) (Vivian and Gibbon 1997) A number of fungal virulence genes have also been discovered: Nectria haematococca (PEP and PDA); tomato leaf mold fungus Cladosporium fulvum (syn. Passalora fulva (Avrs and Ecps); and Magnaporte oryzae (AVR1-CO39) (van der Does and Rep 2007). Pattern-Recognition Receptor Signaling The plant and animal germ-line encoded PRRs of the innate immune system sense through pathogen-associated molecular patterns (PAMPs) the presence of a bacterial, viral or fungal infection (Medzhitov R). One type of PRR, the toll-like receptor (TLR) family, recognizes a vast array of microbial molecules, including lipopolysaccharide (TLR4), bacterial flagellin (TLR5), viral double-stranded RNA (TLR3), and bacterial and viral DNA (TLR9). All PRRs initiate
OCR for page 199
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line signaling pathways that converge at the activation of the transcription factors IRF3, IRF7, and/or NF-B, which leads to the expression of IFN- and the IFN-stimulated genes. Some PRRs also instruct the adaptive immune system, thereby orchestrating an optimal response against the particular pathogen. Viruses more so than bacteria directly interfere with PRR signaling. The importance of this pathway in the control of virus replication is underscored by the identification of greater than 19 inhibitors of PRR signaling encoded by protypic viruses from 9 virus families (Bowie and Unterholzner 2008). Some viruses interfere in the PRR signaling pathway at multiple points as mentioned previously for variola virus (i.e., Cop-M2, Cop-K1, Bsh-D7, Cop-N1 and Cop-A46). Similarly, hepatitis C virus NS3-4A protein inhibits TLR3 signaling though the degradation of TRIF, and the NS5A protein inhibits the activity of IFN-inducible dsRNA-dependent protein kinase, 2’,5’-oligoadenylate synthase, and myeloid differentiation primary-response gene 88. In addition, a single step in the PRR pathway can be targeted by convergent evolution by a number of viruses. Ebola virus VP35, vaccinia virus E3L, influenza virus A NS1 and reovirus σ3 all sequester double-stranded RNA that prevents activation of RIGI and MDA5. Evidence of bacterial pathogens directly interfering with TLR signaling is limited; however there is at least one example of downstream modulation of PRR responses. LcrV is encoded on pYV virulence plasmid common to Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica. Like many virulence factors, LcrV is described to be involved in several functions including regulation of production of Yops and the type III protein secretion system that translocates Yops into host cells. In addition, LcrV is an immunomodulator involved in TNF-α and IFN-γ down-regulation and IL-10 induction through interaction with cell surface CD14/TLR2 (Sing, Reithmeier-Rost et al. 2005). Plant pathogenic bacteria also target plant PRR using mechanisms both unique to plants and conserved in plants and animals. One such conserved mechanism is the delivery of type III effector proteins via a type III secretion system present in P. syringae and other Gram-negative pathogens. There is a great diversity of effectors both within and among bacterial species based on sequence level comparisons; over 30 effectors are likely to be delivered by P. syringae pathovar tomato (Chang, Urbach et al. 2005). One effector, AvrPto, suppresses signaling from the plant surface PRR FLS2 that senses the conserved flg peptide of flagellin (Abramovitch, Anderson et al. 2006). Complement The complement system in mammals consists of more than 35 soluble proteins and receptors that play a key role in innate and adaptive immunity. Complement is activated through three different pathways: alternative, lectin and classical. In innate immunity, the functions mediated by complement activation products include phagocytosis and cytolysis of pathogens, solubilization
OCR for page 200
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line of immune complexes, and inflammation (Walport 2001a, 2001b). The complement system is present in invertebrate species and is at least 600 million years old, which explains the varied mechanisms employed by microorganisms to block or subvert its action. To date bacteria, viruses, fungi, and parasites have been reported to encode 38, 10, 3, and 8 distinct proteins, respectively, which target the complement pathway (Lambris, Ricklin et al. 2008). The activity of these proteins falls into three classes: (1) recruitment or mimicking of complement regulators; (2) modulation or inhibition of complement protein by direct interactions; and (3) inactivation of complement regulators by enzymatic degradation. In addition, bacteria and viruses employ passive features to subvert complement function. The surfaces of certain enveloped viruses such as orthopoxviruses contain host-derived regulators of complement activation, decay-accelerating factor and membrane cofactor protein which block lysis (Moulton, Atkinson et al. 2008). The cell walls of the Gram-positive bacteria such as S. pneumoniae and S. aureus are resistant to membrane-attack complex formation (Joiner, Brown et al. 1983). M. tuberculosis employs a C2a-dependent entry pathway that results in surface deposition of C3b. The opsonized bacteria are taken up into the macrophage via the complement receptor CR3 where they replicate within phagosomes (Schorey, Carroll et al. 1997). Inflammatory/Immune Cytokines Cytokines and chemokines play crucial roles in inducing the migration of inflammatory/immune cells to areas of infection, in antimicrobial defense, and in the orchestration of the adaptive immune response. As such, cytokine/chemokine signaling pathways are key targets of microbial evasion and subversion mechanisms that act inside the cell, at the plasma membrane, and outside the cell. Microbial pathogens block or subvert the intracellular production and/or intracellular signaling of cytokines and chemokines by a number of mechanisms. A common target for microbial pathogens is the transcription factor NF-B. Poxviruses encode 15 unique proteins that inhibit different steps in the signaling pathways leading to NF-κB activation, and an additional 5 proteins that uniquely and directly interact with the NF-κB complex (Mohamed, Rahman et al. 2009). S. flexneri type III secretory system effector OspG and rotavirus NSP1 protein inactivate the cellular E3 ubiquitin ligase complex SCFβ–TrcP, which is required for degradation of IB (Kim, Lenzen et al. 2005; Graff, Ettayebi et al. 2009). YopJ (Y. pseudotuberculosis) inhibits MAPK (mitogen-activated protein kinase) and NF-κB activity. The NF-κB inhibitory activity is likely mediated by yet another unique mechanism as YopJ has homology with the cysteine proteases of the “ubiquitin-like protease” family, and the substrates for YopJ were shown to be highly conserved ubiquitin-like molecules (e.g., SUMO-1) (Orth K). The YopJ family contains proteins found
OCR for page 201
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line in other microorganisms with intimate relationships with eukaryotes, both animals and plants (e.g., adenovirus, adenovirus protease; S. typhimurium, AVrA; plant pathogen, Xanthomonas campestris, AvrBsT). Importantly, the predicted catalytic triad of YopJ and AvrBsT were required for inhibition of MAPK and NF-κB signaling in animal cells and for the induction of localized cell death in plants, respectively (Neish 2004). Viruses also modify the activity of cytokines/chemokines at the plasma membrane prior to engagement of the receptor. For example, herpesviruses and poxviruses collectively encode over 40 viral members of the seven transmembrane–spanning G protein-coupled chemokine receptor superfamily (Sodhi, Montaner et al. 2004). Other classes of viral virulence genes interfere with cell surface binding of cytokines. The poxvirus IFN-α/BP can bind type I IFNs in the extracellular milieu, and can also bind back to the surface of infected or uninfected cells to act as a decoy receptor, preventing the binding of type I IFNs to cellular receptors and the induction of an antiviral response (Xu, RH). Finally, cytokines/chemokines are sequestered or destroyed outside the cells (Alcami 2003). Some pathogens sequester cytokines by soluble, virus homologs of host receptors or binding proteins [e.g., orthopoxviruses have binding proteins for IL-1β, IL-18, TNF, CD30, type I and type II IFNs (Alcami 2003)]. Certain viruses downregulate the cellular synthesis of pro-inflammatory cytokines and/or other antiviral functions of innate cells by expressing viral homologues of cytokines IL-10 (Epstein Barr Virus, BCRF1; orf virus, vIL-10), IL-17 (herpesvirus saimiri, ORF 13), IL-6 (Karposi’s sarcoma-associated herpesvirus, K2), and semaphorin (asinine herpesvirus, SEMA; vaccinia virus A39). Chemokines are also targeted by pathogens in order to disrupt the chemokine gradient that diminishes or blocks the migration of inflammatory cells to a focus of infection in tissue. The chemokine gradient is disrupted by sequestering or destroying the relevant chemokine(s) [e.g., poxviruses, binding proteins for CC-chemokines; herpesviruses, binding proteins for CC-, CXC-, C-, and CX3C-chemokines; Alcami A)] or by the release of pathogen-encoded antagonists or agonists (e.g., poxviruses, antagonist, for CC- and CXC; herpesviruses, agonists for CC-, CCR8, CCR4, and CXCR2; antagonists for C-, CC, CXC, and CX3C-; Alcami A). Another example of this strategy can be found with Streptococcus pyogenes. S. pyogenes has several mechanisms to modulate neutrophil-mediated antibacterial activity, including the targeted degradation of chemoattractant molecules C5a by SCPA (Ji Y) and IL-8, GCP-2 and GROα by spyCEP(Sumby, Zhang et al. 2008). Inflammatory Cell Response Natural killer cells, macrophages, neutrophils, and dendritic cells are key inflammatory cells of the innate response. The latter three cell types are important in the control of both bacterial and viral infections through the release
OCR for page 202
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line of cytokines/chemokines and microbicidal factors, and phagocytosis of the pathogen. Due to the 1-3 micron size of bacteria, phagocytosis is an effective mechanism for bacterial clearance, and has driven the evolution of microbial countermeasures to a number of steps in the phagocytosis pathway. Translocated bacterial effector proteins can kill cells through necrosis (i.e., toxins) or by inducing apoptosis or inhibiting anti-apoptotic signaling, which can prevent necrotic release of proinflammatory signals (e.g., Shigella flexneri, IpaB (Zychlinsky, Kenny et al. 1994); Yersinia pseudotuberculosis, YopJ (Orth K). Other effectors inhibit uptake of microorganisms by disrupting the host cell cytoskeleton (e.g., Y. pseudotuberculosis, YopE and YopH (Fallman, Andersson et al. 1995; Black and Bliska 2000). Certain microorganisms are able to escape from the phagosome and/or block the phagosome-lysosome fusion. L. monocytogenes is an example of a microbe that efficiently escapes the phagosome and replicates in the cytosol. The phagosomal membrane is disrupted by the action of listeriolysin O and two membrane-active phospholipase C enzymes (e.g., phosphoinositol-specific phospholipase C and broad-range phospholipase C encoded by genes plcA and plcB, respectively; (Flannagan, Cosio et al. 2009). M. tuberculosis is an example of a microbe that arrests phagosomal maturation. An array of factors, including the lipids phosphatidylinositol mannoside and lipoarabinomannan, as well as phosphatidylinositol-3-phosphate phosphatase SapM, prevent the transition of early phagosomes to the late and phagolysosomal stages (Flannagan, Cosio et al. 2009). SELECTION PRESSURE Borrelia Relapsing Fever Tick-borne relapsing fever is caused by Borrelia hermsii, a spirochete that infects the Ornithodoros hermsi tick. O. hermsi is a fast-feeding tick that transmits B. hermsii during a blood meal. Characterization of the bacterial surface proteins during different stages of its life cycle revealed that the spirochetes alter their surface in response to their environment (Schwan and Piesman 2002). When the spirochetes are in the gastrointestinal tract of the tick, they express an Outer Surface Protein (Osp) identical to the Osp expressed in their most recent previous mammalian host. The same is true during the first spirochetemic phase of mammalian infection. However, the spirochete undergoes antigenic variation in the host as a mechanism by which to evade the host immune response. As many as 30 different versions of a single Variable Major Protein (Vmp) of B. hermsii have been identified following outgrowth from a single starting cell in the presence of selective pressure. Each round of spirochetemia (relapsing fever) occurs as a result of antigenic variation of the Vmp so that the pathogen can evade the host defenses mounted by the host to overcome the previous fever episode.
OCR for page 203
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line RNA Viruses As noted earlier, filoviruses and highly pathogenic coronaviruses target a variety of host pathways to enhance virus cross-species transmission, host range and virulence. Among filoviruses, these seem to be mediated by mutation driven processes, while coronaviruses utilize a mixture of recombination and mutation driven pathways to evolve and/or acquire new gene functions. Virulence genes encoded by filoviruses and coronaviruses are listed for convenience as targeting several unique and common pathways. Virus-receptor interactions to promote cross species transmission (SARS-CoV S; Filoviruses: role of GP-mediated host range less clear) Proapoptotic genes that contribute to virus induced cell killing and pathogenesis (SARS-CoV-ORF3a/b, ORF6, ORF7a/b, ORF8, S and M glycoproteins; Filoviruses: GP/sGP); Inhibitors of the interferon response, which induces a large number of unique antiviral molecules; (SARS-CoV: nsp1, nsp3(PLP), nsp7, nsp15, ORF3b, ORF6 and N; Ebola Virus: VP24 and VP35) Inhibitors of NF-kB signaling machinery (SARS-CoV: nsp1, PLP) Inhibitors of nuclear import machinery (SARS-CoV-ORF6; Ebola-VP24) Modulators of the ubiquitin ligase system or SUMO modification machinery that regulate a large number of intracellular process; (SARS-CoV: nsp3(PLP) deubiquitinase activity; Ebola VP35-causes increased SUMOylation of IRF7) Modulators of cell cycle and processes associated with transcription, DNA replication and protein synthesis (SARS-CoV nsp1) Immunosuppression of adaptive immunity (Ebola/Marburg: GP immunosuppressive motif; SARS-CoV: lymphopenia and thrombocytopenia-genetic mechanisms unknown) IMMUNODEFICIENCY HIV Infection The classical example of a microbe that suppresses the immune system is the Human Immunodeficiency Virus (HIV-1). Over time after infection with the HIV-1 virus, an untreated person’s helper cells become depleted. If he/she was previously silently infected with Mycobacterium tuberculosis (the agent of tuberculosis or TB), as is an estimated one-third of the world’s population, that individual will no longer be able to contain the replication of the TB organism. Indeed, in Africa, HIV-1-infected people who develop AIDS (Acquired Immune Deficiency Syndrome) as a consequence of a dearth of T-helper cells
OCR for page 204
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line frequently die of tuberculosis. Conversely, in most immunologically normal people who are infected with M. tuberculosis, the bacterium remains walled off in granulomas by a T-helper-cell-dependent host adaptive immune response called cellular immunity. Organ Transplantation For organ transplant recipients, the risk of infection and the type of infection are functions of the degree of immunodeficiency (i.e., type of immunosuppressive regimen) and the use of preventive prophylaxis. Organ transplantation for end-stage organ failure is an effective therapy, but is limited by the availability of donor organs. In 2005, 66,000 kidney transplants, 21,000 liver transplants and 6,000 heart transplants were carried out worldwide (WHO volumes/85/12/06-039370). The use of increasingly potent immunosuppressive agents has reduced the incidence of rejection, but increased the patient’s susceptibility to opportunistic infections. The sources of the infections are from the donor organ, the recipient (preexisting condition), the community or the hospital environment. Although a large number of infectious agents are capable of infecting transplant patients, the majority of infections are caused by the following pathogens: cytomegalovirus, Epstein-Barr virus, adenoviruses, polyomaviruses BK and JC, and Pneumocystis and various fungal species (Fishman 2007). One study documented fungal infections as a major cause of morbidity and mortality with incidence rates ranging from 5 percent among recipients of kidney transplants to as high as 40 percent among recipients of liver transplants (Paya 1993). MICROBIOME Humans are the natural host to a myriad of microorganisms that assemble into complex, largely beneficial communities that outnumber human cells by ten-fold. The dominant forms of human-microbe interactions are those in which microorganisms benefit the host without causing harm (commensal relationships), and relationships in which both host and microorganism benefit (symbiotic or mutualistic relationships). Co-evolution, co-adaptation and co-dependency are features of our relationship with our indigenous microbiota. Our microbiota is ancient and largely conserved in the general types of organisms that inhabit and persist within us for life. Yet, the microbiota in vertebrates is not only often host-specific, it is also compartmentalized to be niche-specific. For example, the gut microbiota and oral microbiota have quite distinct microbial inhabitants. Although possibly germ-free (gnotobiotic) before birth, humans develop a resident microbiota shortly after birth. In the neonatal period, the community assembly process is dynamic and is influenced by early environmental (in particular, maternal) exposures and stochastic effects. The
OCR for page 205
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line composition of the indigenous microbiota evolves in a generally orderly fashion in response to diet and other environmental factors; it is influenced as well by a diverse human genetic background. The bacterial diversity in the human body is striking in its richness of distinct species and strains, but also noteworthy for the limited number of phyla commonly found in indigenous microbial communities. Of the more than 50 bacterial phyla in the environment, only four (Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria) dominate human mucosal and cutaneous habitats, suggesting that strong selective forces have limited diversity over at least hundreds of thousands of years of co-evolution (8-16). Despite this stereotypic assembly process, within a single mammalian species, including Homo sapiens, each individual has a virtually unique microbiome; its composition and the phenotypes expressed affect as well as reflect the overall biological diversity of humans. The human microbiome is the subject of intensive study, including the major international Human Microbiome Project (HMP). Because of advances in DNA sequencing technologies and improvements in bioinformatics, it has become possible to characterize the great diversity in the human microbiota. In 2007, the National Institutes of Health (NIH) launched the Human Microbiome Project (HMP) as one of its major roadmap initiatives. This major scientific endeavor has the following aims: Determine whether individuals share a core human microbiome. Understand whether changes in the human microbiome can be correlated with changes in human health. Develop the technological tools to support these goals. Address the ethical, legal, and social complications raised by human microbiome research. The human microbiome project will add an enormous amount of additional microbial sequence to our already burgeoning databases. This will be invaluable as we continue to sort out the sequences that have real predictive value instead of being merely suggestive because of some degree of relative homology with a putative virulence factor of a Select Agent.
OCR for page 206
Sequence-Based Classiﬁcation of Select Agents: A Brighter Line This page intentionally left blank.