METAGENOMICS: THE SCIENCE OF BIOLOGICAL DIVERSITY K.J. Shelswell

METAGENOMICS: THE SCIENCE OF BIOLOGICAL DIVERSITY

By K. J. Shelswell

(August 2004)

Biological Diversity

For approximately 4.5 billion years, the Earth has been evolving from a barren volcanic landscape into the vibrant globe full of life that it is today. The first forms of life, small microorganisms, have been found in fossils from 3.5 billion years ago. Around 1.5 billion years ago, motile microorganisms emerged allowing life to migrate to different environments with different environmental conditions like increased exposure to ultraviolet radiation or higher temperatures. Microorganisms began to evolve with the changing environmental conditions of the planet.

These new environmental conditions, acting as selective pressures, drove the evolutionary process. They forced new species of organisms to evolve that were better suited to survival under particular environmental pressures. The evolution of new species generates biological diversity, which is represented by the number of different species in an environment. Over time, the evolutionary process has led to the development of more complex life forms such as trees, fish, and humans. A simple example of biological diversity is a comparison between a human and a monkey (see Figure 1).

Figure 1. The visible differences between a human & a monkey.

Both species (human and monkey) are eukaryotes, multicellular, vertebrates, mammals, and primates. However, significant differences between humans and monkeys are immediately visible such as body hair and arm length. Other differences such as amino acid synthesis cannot be perceived by casual observation. The basis of this biological difference lies in the organization and expression of the genetic material of each species.

Genetic Diversity

DNA is responsible for encoding the physical characteristics of an organism. Differences in DNA sequences between organisms create genetic diversity. These changes are also responsible for the subtle differences (such as hair colour, eye colour, or height) between organisms of the same species. This genetic diversity is able to manifest itself as biological diversity through the structure, organization, regulation, and expression of DNA. These effects determine how organisms develop physically, assimilate nutrients, interact with the environment, and even, in some cases, how they behave (see Figure 2).

Figure 3. How genetic diversity affects biological diversity.

It is these properties of genetic diversity that support the effective stability of natural environments. Multiple biological and non-biological components interact through intricate nutrient cycling webs to create a macroscopic global environment. This global environment can be imagined as a pyramid in which the entire structure depends on each of the small blocks that are used to create and support the larger structure. For this reason, it is often useful to examine the environmental impacts of small ecological components such as microorganisms. As noted above, microorganisms are believed to be the origins life on the planet. This theory is supported by the fact that they display the highest degree of biological diversity.

Metagenomics

To understand the biochemical processes of life, it is often easier to study them in a simple system (like a microorganism) instead of a complex one (like humans). Microorganisms have many of the same properties as more complex organisms such as amino acid biosynthesis. They also contain unique properties such as the ability to degrade waste products. As a result, the genetic and biological diversity of microorganisms is an important area of scientific research. Unfortunately, scientists are able to grow less than 1% of all microorganisms observable in nature under standard laboratory conditions. This leaves scientists unable to study more than 99% of the biological diversity in the environment. Metagenomics is a new field combining molecular biology and genetics in an attempt to identify, and characterize the genetic material from environmental samples and apply that knowledge. The genetic diversity is assessed by isolation of DNA followed by direct cloning of functional genes from the environmental sample.

Metagenomics is described as “the comprehensive study of nucleotide sequence, structure, regulation, and function”. Scientists can study the smallest component of an environmental system by extracting DNA from organisms in the system and inserting it into a model organism. The model organism then expresses this DNA where it can be studied using standard laboratory techniques.

Metagenomics is employed as a means of systematically investigating, classifying, and manipulating the entire genetic material isolated from environmental samples. This is a multi-step process that relies on the efficiency of four main steps (see Figure 3). The procedure consists of (i) the isolation of genetic material, (ii) manipulation of the genetic material, (iii) library construction, and the (iv) the analysis of genetic material in the metagenomic library.

Figure 3. The standard steps of a metgenomics experiment.

The first step of the procedure is the isolation of the DNA. First, a sample is collected that represents the environment under investigation because the biological diversity will be different in different environments. The samples contain many different types of microorganism, the cells of which can be broken open using chemical methods such as alkaline conditions or physical methods such as sonication. Once the DNA from the cells is free, it must be separated from the rest of the sample. This is accomplished by taking advantage of the physical and chemical properties of DNA. Some methods of DNA isolation include density centrifugation, affinity binding, and solubility/precipitation.

Once the DNA is collected, it is manipulated so that it can be used in the model organism. Genomic DNA (the genetic material of an organism) is relatively large so it is cut up into smaller fragments using enzymes called restriction endonucleases. These are special enzymes that cut DNA at a particular sequence of base pairs. The enzymes move along the long fragments until they recognize these sequences where they cut both strands of the DNA. This results in the smaller, linear fragments of DNA depicted in Figure 2. The fragments are then combined with vectors. Vectors are small units of DNA that can be inserted into cells where they can replicate and produce the proteins encoded on the DNA using the machinery that the cells use to express normal genes (see Figure 3). The vectors also contain a selectable marker. Selectable markers provide a growth advantage that the model organism would not normally have (such as resistance to a particular antibiotic) and are used to identify which organisms contain vectors and which ones do not.

The third step is to introduce the vectors with the metagenomic DNA fragments into the model organism. This allows the DNA from organisms that would not grow under laboratory conditions to be grown, expressed, and studied. The DNA inserted in the vector is transformed into cells of a model organism, typically Escherichia coli. Transformation is the physical insertion of foreign DNA into a cell, followed by stable expression of proteins. It can be done by chemical, electrical, or biological methods. The method of transformation is determined based on the type of sample used and the required efficiency of the reaction. The metagenomic DNA in the vectors are all in the same sample initially but the vectors are designed so that only one kind of DNA fragment from the sample will be maintained in each individual cell. The transformed cells are then grown on selective media so that only the cells carrying vectors will survive. Each group of cells that grows is called a colony. Each colony consists of many cloned cells that originated from one single cell. These samples of cells containing all of the metagenomic DNA samples on vectors are called metagenomic libraries. Each colony can be used to create a stock of cells for future study of a single fragment of the DNA from the environmental sample.

The fourth and final step in the procedure is the analysis of the DNA from the metagenomic libraries. The expression of DNA determines the physical and chemical properties of organisms so there are many potential methods of analysis. A phenotype is the physical attribute associated with expression of a gene. An example of metagenomic analysis would be to look for an unusual colour or shape in the model organism. An aspect of the phenotype that is not readily observed is chemical reaction. The chemical properties of the expressed metagenomic DNA can be examined by performing chemical assay on products created by the model organism. This would investigate whether the model organism gained an enzymatic function that it was previously lacking such as use of an unusual nutrient source for growth under conditions that limit normal nutrient availability.

Metagenomic libraries are typically used to search for new forms of a known gene. First, the metagenomic DNA is inserted into a model organism that lacks a specific gene function. Restoration of a physical or chemical phenotype can then be used to detect genes of interest. A genotype is the specific sequence of the DNA and provides another means of analyzing the metagenomic DNA fragment. The sequence of the bases in the DNA can be compared to databases of known DNA to get information regarding the structure and organization of the metagenomic DNA. Comparisons of these sequences can provide insight into how the gene products (proteins) function.

Genotypic analysis is usually performed after phenotypic analysis. A typical metagenomic analysis involves several subsequent rounds of the procedure in order to definitively isolate target genes from environmental samples and to effectively characterize the information encoded by the DNA sequence. The information gained from the metagenomic procedure provides information regarding the structure, organization, evolution, and origin of the DNA and can be used in scientific applications for the benefit of society and the environment

Applications of Metagenomics

Many microorganisms have the ability to degrade waste products, make new drugs for medicine, make environmentally friendly plastics, or even make some of the ingredients of food we eat. By isolating the DNA from these organisms, it provides us with the opportunity to optimize these processes and adapt them for use in our society. As a result of ineffective standard laboratory culture techniques, the potential wealth of biological resources in nature (like microbes) is relatively untapped, unknown, and uncharacterized. Metagenomics represents a powerful tool to access the abounding biodiversity of native environmental samples. The valuable property of metagenomics is that it provides the capacity to effectively characterize the genetic diversity present in samples regardless of the availability of laboratory culturing techniques. Information from metagenomic libraries has the ability to enrich the knowledge and applications of many aspects of industry, therapeutics, and environmental sustainability. This information can then be applied to society in an effort to create a healthy human population that lives in balance with the environment. Metagenomics is a new and exciting field of molecular biology that is likely to grow into a standard technique for understanding biological diversity.

Information References

1.Kimball J. Kimball’s Biology Pages: Taxonomy.

2. Jasper S. University of Texas: Life Sciences.

3. Vogel TM, Nalin R (2003). Sequencing the metagenome. ASM News 69(3):107.

VIRUS SCHMALLENBERG 2012

Un nuevo virus llamado Schmallenberg ALEMANIA : En verano-otoño del año pasado, ganaderos y veterinarios de la región alemana de Renania-Westfalia, en particular de algunas granjas en la localidad de Schmallenberg, detectaron que algo no iba bien en sus vacas lecheras: tenían fiebre y diarrea, y producían menos leche. Enviaron muestras de los animales enfermos al laboratorio de referencia dentro de su red nacional de vigilancia sanitaria veterinaria (que corresponde al Friedrich Löeffer Institute, de Riems), para que investigaran qué podía estar ocurriendo. Tras descartar enfermedades conocidas y que podían tener consecuencias graves para el ganado (pestivirosis, lengua azul, fiebre aftosa, fiebre del Valle del Rift, etc) decidieron estudiar el caso en mayor profundidad. Si esto hubiera ocurrido hace tan solo 3 ó 4  años, habría pasado lo siguiente: el laboratorio de referencia habría aplicado todas las técnicas disponibles para los agentes infecciosos más probables, o incluso no tan probables, que pudieran afectar al ganado. Habrian podido también emplear pruebas “genéricas” que permiten detectar la presencia de grupos de patógenos relacionados a nivel genético. Podrían incluso haber aplicado pruebas de aislamiento vírico y técnicas de microscopía electrónica, y con suerte podrían haber detectado algún virus con una morfología característica que podría haber sido asignado a un grupo concreto de virus con los que compartiera esa morfología. En este último caso, prosiguiendo esos estudios, quizá durante varios meses, o incluso más tiempo, se podría haber llegado a alguna conclusión sobre la identificación de un “nuevo virus”. Sin embargo, lo más probable es que de estas investigaciones se hubiera obtenido un resultado  ”no concluyente” (por no obtener resultados tras las pruebas genéticas y el aislamiento vírico, por ejemplo, algo muy probable en este caso), y salvo que la enfermedad persistiera en gravedad y/o se extendiera, el caso se “archivaría” hasta encontrar más pruebas. Pero estamos en 2012, y lo que ha ocurrido es esto: el Friedrich-Löeffer Institut (FLI) es un centro dotado con los ultimos avances tecnológicos. Entre ellos posee desde hace poco tiempo una tecnología realmente novedosa, que se conoce como metagenómica y que no vamos a explicar aquí (hay bonitos vídeos en YouTube, como el del siguiente enlace que explican cómo funciona). Esencialmente consiste en “leer” las secuencias de nucleótidos de los ácidos nucléicos (ADN y ARN) presentes en la muestra. Ya sé que esto ya lo hacían otras máquinas, pero la novedad de esta es que lee TODAS las secuencias de nucleótidos que encuentra en la muestra, de una sola vez. Para que se hagan una idea, si con las tecnologías convencionales de la época se tardó aproximadamente 13 años en secuenciar el primer genoma humano completo (unos 6000 millones de nucleótidos), y costó unos 2000 millones de €, en la actualidad, esto es, 11 años después de ese hito, la metagenómica permite hacer ese trabajo en una semana por unos 2000 €. Pues bien, con esta maravillosa máquina los científicos del FLI  examinaron las muestras de las vacas enfermas. La máquina da como resultado algo un poco abstracto (cientos de miles de lecturas de secuencias cortas solapantes que hay que ir empalmando, como si se tratara de un auténtico rompecabezas). Para entendernos, nos da un “ovillo” y de ahí hay que sacar el “hilo”, es decir, la secuencia del agente patógeno que podría causar la enfermedad. Unas secuencias peculiares llamaron la atención de los investigadores alemanes: en el ovillo había secuencias de un tipo de virus, de la familia de los Ortobunyavirus, que no es habitual en Europa, y del que se sabe que algunos representantes pueden infectar a las vacas y producirles una enfermedad. Con todas las secuencias obtenidas lograron “tirar del hilo” y reconstruir la secuencia completa de ARN del virus, y las compararon con las secuencias similares que había disponibles en las bases de datos públicas. Se trataba de un virus muy parecido al virus Shamonda, otro ortobunyavirus dentro del serogrupo Simbu, que afecta a bovinos y que fué aislado en Japón. El saber a qué virus se parece ayuda mucho en las investigaciones: estos virus al parecer son transmitidos por picaduras de artrópodos, probablemente Culicoides (como la lengua azul) o mosquitos. También parece que se transmite por la vía  transplacentaria. Del mismo modo, los conocimientos sobre la secuencia del nuevo virus y su parecido con otros ortobunyavirus del mismo serogrupo han ayudado en el aislamiento del mismo en cultivo, que se ha conseguido en células derivadas de un posible vector Culicoides. El virus aislado o tomado de muestras de animales infectados ha sido inoculado en vacas, que han desarrollado la infección y los signos clínicos de la enfermedad, lo que da cumplida cuenta de los postulados de Koch para este virus y la enfermedad que produce. Este nuevo virus ha recibido el nombre provisional de virus Schmallenberg por la localidad alemana donde ha sido descrita su presencia por primera vez. Decimos “provisional” porque no sería la primera vez (ni será la última) que los habitantes de una localidad se niegan a que un virus tome el nombre de la misma, porque no les gusta verse asociados a algo tan negativo como una enfermedad infecciosa, una “peste”, en definitiva (pueden encontrar más información acerca de la dificultad de nombrar a los virus en el siguiente enlace). Una vez se ha reconstruido la secuencia del virus emergente es posible avanzar muy rápido: desarrollar pruebas que permitan su diagnóstico rápido es coser y cantar. De este modo en pocas semanas los científicos del FLI pudieron investigar con técnicas específicas la presencia del nuevo virus en otras granjas cercanas, así como en casos de enfermedad compatible con la clínica observada. En pocos meses se ha podido investigar la expansión de la enfermedad en Europa. En esto ha ayudado bastante el que los investigadores del FLI han compartido la información y puesto a disposición de la comunidad científica todas las herramientas desarrolladas, de un modo muy rápido y eficaz. Actualmente la práctica totalidad de los laboratorios nacionales de referencia de los países de la UE, incluyendo el nuestro, tienen ya las herramientas que permiten la detección rápida del virus, lo cual permite una vigilancia efectiva. Hasta el momento se ha detectado el virus en Alemania, Holanda, Bélgica, Reino Unido y Francia. Se ha comprobado que no solo infecta a bovinos, sino que también las ovejas y las cabras son susceptibles a la enfermedad, produciendo en ellas abortos y malformaciones congénitas. Seguramente a estas alturas se estarán haciendo muchas preguntas: ¿de donde ha salido este virus? ¿por qué ha aparecido en Alemania? ¿que hubiera pasado si no se hubiera empleado la metagenómica? ¿en los países donde no se emplea aún esta tecnología, pasan desapercibidos muchos virus? Creo que, para no extendernos mucho, estas preguntas las podemos dejar para otros post. Únicamente me gustaría acabar remarcando el ejemplo que constituye el descubrimiento de este virus por la poderosa tecnología metagenómica. En los ultimos años se han descubierto un gran número de virus nuevos empleando esta tecnología, y seguramente los años venideros aguardan el descubrimiento de muchos más virus hasta ahora desconocidos, y que pasarán al bando de los “virus emergentes” en el momento que sean descubiertos.

BACTERIÒFAGOS

Bacteriófagos, enemigos de las bacterias

( Publicado en Revista Creces, Diciembre 1996 )

Las bacterias se han vuelto resistentes a los antibióticos y estos ya no las pueden combatir. Descubrir nuevos antibióticos ya se hace difícil. Es necesario desarrollar una nueva estrategia y ella puede estar en los virus. Desde hace ya tiempo que se sabe de la existencia de virus enemigos de las bacterias, y con ello podemos asociarnos.

Como atacar a las bacterias

El descubrimiento de los antibióticos, que se inició en Ia década de los 40 y que llegó a suauge en los 80, pareció ser el golpe definitivo contra las bacterias que producían enfermedades infecciosas en eI hombre y los animales. El mecanismo se basaba, en general, en la utilización de sustancias químicas que eran capaces de interferir en alguna etapa metabólica de las bacterias haciendo imposible su viabilidad. Para la selección de estas sustancias se requería también de otra condición: que estas mismas no interfirieran en el metabolismo de las células humanas o animales. Con esta idea "in mente" se descubrieron numerosas sustancias químicas que cumplían con estos objetivos. Porque ellas bloqueaban el proceso vital de las bacterias se les llamó antibióticos.

Todo iba bien encaminado, hasta que se comenzó a notar que algunas bacterias poseían medios de sobrevivencia que les permitían ser resistentes a los antibióticos. Normalmente, cuando se produce una infección bacteriana la administración de antibióticos permite bloquear su metabolismo, pero sin embargó entre ellas hay algunas resistentes que logran sobrevivir. Ello debido a que poseen un trozo de DNA (plasmidio) que contiene una instrucción que permite desarrollar un mecanismo de degradación e inactivación del antibiótico. Ellas son escasas, pero solidarias, de modo que traspasan esta información a aquellas que son sensibles y de esta manera aumenta el número de bacterias resistentes.

Hasta ahora, en la medida que las bacterias se iban haciendo resistentes a algún antibiótico, se buscaban nuevos, para los cuales ellas no tenían resistencia. Sin embargo, esta veta parece agotarse, ya que cada día se hace más difícil descubrir nuevos antibióticos. Lo que era sólo un temor se está haciendo una realidad y existen posibilidades ciertas de que sean las bacterias las que terminen ganando Ia guerra.

Ya son muchas las bacterias que son resistentes a uno ó varios antibióticos. Unas de las que se han hecho más resistentes son los neumococos, gérmenes causantesl de infecciones al oído, neumonías, infecciones de Ia sangre y aun meningitis. Otros son los estafilococos, que son los gérmenes mas frecuentes de las infecciones de la piel, heridasy también causan infecciones de la sangre. También los enterococos, que refugiándose en los hospitales producen infecciones urinarias y de las heridas. El estreptococo, que produce infecciones a la garganta, escarlatina y neumonía. El Vibrio cholera, que produce el cólera, y finalmente el Mycobacterium tuberculosis, que produce la tuberculosis y que en la actualidad está infestando a casi un terció de Ia población mundial. Su resistencia a los antibióticos está en gran medida causando anualmente Ia muerte a más de 3 millones de personas.


Hay virus amigos que pueden ayudar

Ante esta realidad se ha pensado en otra estrategia. Ella no es nueva, porque se conocíaya desde hace algunos años: utilizar virus que son enemigos de las bacterias. A los viruslos hemos mirado siempre como nuestros enemigos, ya que producen diversas enfermedades que aun son más difíciles de tratar que las producidas por las bacterias. Pero si algunos son enemigos nuestros, otros son también enemigos de las bacterias. "El enemigo de mi enemigo, es mi amigó". Con esta filosofía ha surgido Ia idea de asociarnos a los virus enemigos de bacterias, para que ellos nos ayuden a atacarlas.

Los virus son elementos más pequeños que las bacterias. Una bacteria promedio mide un micrón (una milésima de un milímetro). Un virus, en cambió, mide Ia cuarenta ava parte de un micrón. Son tan pequeños que sólo los podemos ver gracias al microscopio electrónico.

Están constituidos por un pequeño trozo de DNA o RNA, envuelto por capas de proteínas. Ellos no son capaces de sobrevivir por si mismos, y necesitan introducirse aI interior de las células y profitar de todo eI sistema productivo de ellas. Es así como en su interior proliferan en grado tan abusivo que terminan por matar las células que los cobijó (Creces Nº 3). Diversos virus específicos son capaces de infestar también células específicas, sean éstas vegetales o animales.

Pero las bacterias son también células, pero sin núcleo, y ellas también son atacadas porvirus específicos. Estas virus que devoran y matan a las bacterias se han denominado bacteriófagos o, para ser más corto "fagos".


Los fagos y su historia

La existencia de los fagos ya se sospechaba desde hace varios años. En 1917, eI bacteriólogo canadiense-francés, quien trabajaba en el lnstituto Pasteur de París, Felix d`Herelle investigando un brote de disentería, encontró algo que le pareció muy raro; al cultivar las bacterias de la disentería y luego pasar el líquido de cultivo turbio por filtros, de pronto éste se clarificaba completamente. Dos años antes el bacteriólogo inglés, Frederick Twort había observado el mismo fenómeno, pero no pudo darle ninguna explicación. En cambio d`Herelle pareció encontrar una que parecía razonable: "Io que causa el aclaramiento de las cultivos son microbios invisibles, un virus parásito de Ia bacteria". El, por primera vez, los llamó "virus".

No deja de ser admirable esta intuición de d´Herelle, ya que en aquella época no se conocían los virus, y nadie los había visto, por Ia sencilla razón de que no se contaba con Ia microscopía electrónica. Su explicación produjo impacto en Ia época, ya que el NewYork Times, en 1925 publicó el siguiente titular: "Los pequeños y mortíferos bacilos tienen enemiqos todavía más pequeños".

En el año 1920, este mismo investigador ideó tratar pacientes de cólera con un bacteriófago específico. Las primeras experiencias parecían favorables, pero luego abandonó la investigación cuando los antibióticos hicieron su triunfal aparición.

Más tarde, cuando se pudo observar los fagos al microscopio electrónico, la hipótesis se fue consolidando. Se observó que los fagos tenían una forma muy especial, con una gran cabeza en cuyo interior guardaban su DNA y una larga cola. Era la cola la que apoyaban en Ia pared de Ia bacteria y, a través de ella como por un tubo, introducían sus genes al interior de Ia bacteria. Allí aprovechaban la maquinaria de ella y se reproducían en gran cantidad hasta destruirla. Más tarde estos nuevos fagos ya Iiberados se introducían a nuevas bacterias, repitiendo así el ciclo aniquilador.


Como utilizar los fagos

Ya se han iniciado los trabajos experimentales, y es así como Carl Merril, Sandra Adhya ycolaboradores, todos del National Institute of Health de Bethesda (Maryland), trabajando con la empresa Exponential Biotherapies, han demostrado que ratas infectadas con bacterias que para ellas son letales, pueden curarse si al mismo tiempo se les administra algunos fagos muy bien seleccionados (New Scientist, Abril 27, 1996, pág. 16).

Esto de seleccionar fagos no es fácil, porque para cepas específicas de bacterias se requiere también de fagos específicos que las ataquen y éstos hay que buscarlos yseleccionarlos.

Cuando las fagos se utilizan por vía oral no hay problemas. Sin embargo, cuando los fagos entran al torrente circulatorio son rápidamente captados por los macrófagos, que son glóbulos blancos que se encuentran en gran cantidad en el bazo, el hígado y Ia médula ósea. No obstante, los investigadores creen que ello es solucionable, ya que el ataque se debería a que los fagos utilizados no estaban absolutamente purificados ylibres de toxinas, que son las que llaman la atención de los macrófagos. 

Estos investigadores han estado trabajando también con un fago especial llamado "Pambda" que es capaz de infestar específicamente a Ia Escherichia coli que produce trastornos digestivos. Esta bacteria se encuentra normalmente en eI intestino, pero en ocasiones también puede producir infecciones urinarias e incluso septicemias (infecciones de Ia sangre). Ellos purificaron cuidadosamente los fagos para extraerles posibles toxinas y luego los inyectaron a ratas a las que previamente se les habíasuministrado una dosis fatal de E.coIi. Los animales enfermaron, pero no murieron. 

Los investigadores han logrado mayores éxitos seleccionando algunas cepas especiales de fagos, que Iogran sobrevivir más tiempo en el torrente circulatorio. Dos de estas cepas, la llamada Argo 1 y Argo 2, produjeron tan buen resultado que ratas que recibieron dosis fatales de E. coli no sólo sobrevivieron sino que además presentaron sintomatologías muy atenuadas (Proceedings of the National Academy of Science, vol. 93, 1996, pág. 3189).

En la actualidad están ensayando fagos para tratar enfermedades producidas por bacterias resistentes a múltiples antibióticos. Una de esas bacterias es el Enterococo y el Stafilococo, ambos gérmenes difíciles de combatir porque han llegado a ser resistentes a múltiples antibióticos. Los resultados han sido muy interesantes. Los mismos investigadores están tratando de usar fagos para combatir bacterias resistentes de la tuberculosis, que hoy está produciendo estragos.

En fin, los fagos parecen muy atractivos, ya que no producen reacciones alérgicas, como muchos antibióticos y, además, no hay que preocuparse de Ia dosis, ya que basta una sola administración para que ellos capten la bacteria correspondiente y en su interior se multiplican hasta que éstas desaparecen. Por Io tanto, tampoco las bacterias tienen oportunidad de crear resistencia a los fagos. El único problema es que para cada bacteria hay que administrar el fago específico, lo que no sucede con los antibióticos que tienen un amplio espectro de acción. Ello se puede hacer, pero cada caso lleva tiempo, ya que primero hay que individualizar el germen causante de Ia enfermedad y Iuego suministrar el fago específico.

Ya son numerosos los grupos de investigadores que están trabajando en este campo (Discover, Noviembre 1996, pág. 45) y por Io general han sido muy promisorios los resultados que están obteniendo. Parece ser que los fagos son un nuevo camino, yevidentemente hay que recuperar su uso. Tal vez estemos iniciando una nueva era, post antibióticos.

VIRUS: CONGRESO EN AUSTRALIA Juan Kuznar H.

Australia

• XI Congreso Internacional de Virología

Durante una semana se reunieron en Sidney, Australia, los más destacados investigadores del mundo cuyo trabajo de alguna forma u otra está vinculado a los virus. Ya sea por que estos microorganismos se utilizan como modelos para responder trascendentes preguntas de las ciencias biológicas o por la necesidad de conocer sus puntos débiles con el objeto de contrarrestar sus nocivos efectos sobre salud, ecología o economía.
La investigación virológica tiene la especial atracción que el sujeto de estudio es un organismo cuya capacidad de adaptación no tiene competencia entre los seres vivos. Lo que a otras especies les cuesta miles o millones de años de evolución, a los virus puede bastarle semanas o meses para fijar algún cambio que les dé nuevas ventajas respecto de sus pares y las cuales, a menudo, significan problemas para los seres humanos, por ejemplo.
Parte importante de las sesiones del congreso estaban relacionadas con el mayor o menor éxito que hemos tenido en el control de las enfermedades. Hay algunos triunfos espectaculares que significan enormes avances en la medicina. En Febrero del año 2000 se cumplirán 50 años desde que se administró la primera vacuna oral para prevenir la polio en 20 niños. Hoy se puede decir que la enfermedad paralítica está a punto de ser erradicada del planeta. Sin embargo, esto no significa que el virus propiamente tal está eliminado.
Los virus tienen recursos muy sofisticados para eludir los cercos tecnológicos con que pretendemos controlarlos. Producir una vacuna contra la infección por el virus de la inmunoinsuficiencia humana, HIV, ha resultado extremadamente complicado. Algunos virus pueden ser controlados por los linfocitos T citotóxicos, de hecho la primera gran caída de la concentración de virus HIV en humanos se debe a una vigorosa respuesta de estas células. Lamentablemente, ésta es insuficiente para evitar el progreso de la enfermedad.
Una de las preguntas claves a responder para intentar diseñar una vacuna anti-HIV es, ¿Por qué los linfocitos T citotóxicos no pueden detener el progreso de la enfermedad? Lo que hasta este momento se conoce es que el virus HIV tiene la capacidad de impedir que la célula infectada "muestre" al sistema inmune que efectivamente está infectada. Lo hace interfiriendo con el mecanismo molecular que tienen las células para exponer en su superficie señales que indican que están infectadas. El virus interfiere con el tráfico de un selecto grupo de moléculas, HLA y HLB, que viajan hacia la superficie de la célula con péptidos virales que el sistema inmune reconoce como extraños y además peligrosos.
Conocer estos mecanismos permite plantear estrategias racionales de vacunación dirigidas a eludir estos trucos de los virus. Es así como los diseñadores de vacunas contra HIV están considerando nuevos agentes inmunolóicos para obtener poderosas respuestas de los linfocitos T citotóxicos.
Para sostener el crecimiento de la población humana en nuestro planeta se efectúan enormes esfuerzos para una agricultura cada vez más eficiente y productiva. Un serio factor limitante es la gran variedad de virus que producen cuantiosas pérdidas en los cultivos. Este fue otro importante tema de discusión en el congreso. El de los avances en el conocimiento de las complejas relaciones entre los virus y los vegetales que ellos infectan.
Se han identificado genes de plantas que están vinculados con mecanismos de defensa contra la invasión viral, sin embargo, adicionalmente, y como ocurre con los virus animales, los virus de plantas también poseen sofisticados mecanismos moleculares que pueden disminuir seriamente la operatividad del sistema inmune vegetal.
Del estudio de estas complejas relaciones virus - planta, surgirán en forma natural vías para aumentar el efecto de los genes protectores, asR como, también, reducir el efecto de los genes virales que se oponen a los anteriores. La estrategia más promisoria para el control de los virus vegetales, es, por el momento, la de generar plantas transgénicas en las cuales se incorporan genes que aumentan su resistencia. Se ha tenido un importante éxito en la protección contra virus que afectan a la producción de papayas y de plátanos en Australia.
El conocimiento detallado de los mecanismos de control de la expresión genética de los virus es fundamental para desarrollar estrategias terapéuticas o preventivas contra las enfermedades virales. Un excelente ejemplo fue presentado en el congreso. Un importante grupo de patógenos está constituido por virus cuyo genoma consiste en una cadena de RNA negativo.
Estos virus cuando se multiplican en la célula infectada necesitan generar un número muy preciso de los diferentes componentes que permiten el ensamblaje del virus. La preservación de esta estoiquiometría molecular es posible debido a una forma de control transcripcional que implica que los genes virales se expresan más eficientemente en la medida que estén más cerca del extremo 3' donde está el promotor. Las proteínas que se necesitan en mayor cantidad están codificadas, entonces, hacia el extremo 3' del genoma viral.
Lo interesante de este descubrimiento es que si se altera biotecnológicamente el orden de los genes, también se altera las cantidades relativas de las proteínas que se sintetizan, resultando de esto que se ensamblan muchos viriones defectuosos con una muy reducida patogenicidad. Lo importante de este resultado es que se obtienen variantes de virus que se caracterizan por una nula o muy baja patogenicidad, pero, con una alta capacidad para estimular el aparato inmune del animal infectado. De esta manera es posible diseñar excelentes vacunas mediante esta estrategia. Los resultados preliminares en animales de experimentación son muy alentadores.
Los virus no son solamente agentes catastróficos, también se presentaron trabajos relativos a la posibilidad de usar a virus como mediadores en la transferencia de genes destinados a corregir enfermedades. Dentro de lo que se denomina medicina molecular la terapia genética ocupa un destacadísimo lugar.
Algunos virus son excelentes vectores para introducir genes en células. Uno de los problemas técnicos de mayor envergadura es el de poder introducir genes terapeúticos en células que no están en división. En una de las sesiones plenarias se mostró que se puede utilizar vectores basados en los lentivirus para introducir en forma estable y por supuesto sin producir enfermedad alguna, genes correctores en células tanto in vitro como in vivo. El procedimiento tiene pleno éxito en la introducción de genes foráneos en cerebro, músculo, retina y células hematopoiéticas. En todos los casos con la corrección de los defectos genéticos previamente existentes.
Una de las enseñanzas más importantes del último congreso mundial de virología de este milenio es que los virus representan una enorme paradoja para el futuro. Por un lado, grandes amenazas de enfermedades virales emergentes producto de las modificaciones que introducimos al ambiente y en nuestras costumbres. Por otro lado, ciframos en su manejo biotecnológico grandes esperanzas en un impacto positivo en la medicina humana, veterinaria y en la agricultura a través de su uso como vector de genes o para contrarrestar el efecto de otros agentes patógenos.
Dr. Juan Kuznar H.
jkuznar@uv.cl Profesor de Bioquímica y Virología Facultad de Ciencias Universidad de Valparaíso Valparaíso, Chile

LA PLAGA Y EL CLIMA Tamara Ben et al 2011

Plague and Climate: Scales Matter

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Tamara Ben Ari^1,2, Simon Neerinckx¹, Kenneth L. Gage³,Katharina Kreppel⁴, Anne Laudisoit⁵, Herwig Leirs⁵, Nils Chr. Stenseth^1*

1 Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway, 2 Ecole Normale Supérieure, CNRS UMR 7625, Paris, France, 3Bacterial Diseases Branch, Division of Vector-Borne Diseases, Center of Control and Prevention, Fort Collins, Colorado, United States of America, 4Liverpool University Climate and Infectious Diseases of Animals Group (LUCINDA), Department of Veterinary Clinical Sciences, University of Liverpool, Leahurst, Great Britain, 5 Evolutionary Ecology Group, Department of Biology, Universiteit Antwerpen, Antwerp, Belgium

Abstract Top

Plague is enzootic in wildlife populations of small mammals in central and eastern Asia, Africa, South and North America, and has been recognized recently as a reemerging threat to humans. Its causative agent Yersinia pestis relies on wild rodent hosts and flea vectors for its maintenance in nature. Climate influences all three components (i.e., bacteria, vectors, and hosts) of the plague system and is a likely factor to explain some of plague's variability from small and regional to large scales. Here, we review effects of climate variables on plague hosts and vectors from individual or population scales to studies on the whole plague system at a large scale. Upscaled versions of small-scale processes are often invoked to explain plague variability in time and space at larger scales, presumably because similar scale-independent mechanisms underlie these relationships. This linearity assumption is discussed in the light of recent research that suggests some of its limitations.

Citation: Ben Ari T, Neerinckx S, Gage KL, Kreppel K, Laudisoit A, et al. (2011) Plague and Climate: Scales Matter. PLoS Pathog 7(9): e1002160. doi:10.1371/journal.ppat.1002160

Editor: Marianne Manchester, University of California San Diego, United States of America

Published: September 15, 2011

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Funding: The authors received no specific funding for this study.

Competing interests: The authors have declared that no competing interests exist.

* E-mail: n.c.stenseth@bio.uio.no

Introduction Top

Plague is a rapidly progressing infectious disease that is infamous for having caused the death of millions of people in large historic pandemics [1] as well as numerous other deadly but localized outbreaks [2]. Plague, caused by the pathogenic bacterium Y. pestis is transmitted from host to host by fleas via blood feeding, through consumption or handling of infectious host tissues, or through inhalation of infectious materials. Plague is thought to persist for long periods of time at low to very low levels of prevalence in so-called enzootic cycles that cause little host mortality and involve partially resistant rodents (often called enzootic or maintenance hosts). These long periods are punctuated by occasional outbursts or epizootics (i.e., spreading die-offs) among these hosts or epidemics, when the incidence among humans increases. Figure 1 illustrates these intertwined cycles.

Figure 1. Schematic of the plague cycle with small mammals as hosts and fleas as vectors.

Arrows represent connections affected by climate with a color-coding depending on the most influential climate variable on this link (i.e., precipitation, temperatures, and other variables indirectly depending on them such as soil characteristics and soil moisture). Grey rectangles somewhat arbitrarily delimit epizootic, enzootic, and zoonotic cycles. Note that despite their location at the far end of the cycle, humans often provide the only available information on plague dynamics.

doi:10.1371/journal.ppat.1002160.g001

Climate has long been suspected to be a key factor in the alternation between quiescent and active periods of plague. Rogers (1928) suggested seasonal variations in temperature and humidity to be responsible for the seasonal patterns of human plague incidence in India [3]. Decades later, Davis showed that human plague outbreaks in several African countries were less frequent when the weather was too hot (>27°C) or cold (<15°C) [4]. Subsequent studies showed an increased plague incidence in Vietnam during the hot, dry season, when following a period of high seasonal rainfall [5],[6]. Nowadays, several studies, as we report here, demonstrate climate's impacts on plague incidence spatial and temporal variability.

In the context of public health and wildlife conservation, we need an improved understanding of the mechanisms underlying the association between plague outbreaks and climate. As we will show in this review, this understanding is only partially available at present. There are several reasons for this. First and perhaps most importantly, the plague cycle is complex. It is composed of three components that interact with each other and all are influenced by climate variables with a broad range of times lags. Also, climate variability manifests itself at numerous temporal and spatial scales that condition the form of the response in plague dynamics. To cope with this series of difficulties, we break down the problem as follows: in section 1 we review individual effects of climate variables on each of the plague components. Our knowledge of these effects is primarily based on small-scale studies that are useful because they provide conceptual models for how larger scale climate variability may force the plague system. The way these conceptual models are most often used raises the issue of upscaling conclusions by inference from the results of small scale studies, a subject on which we focus on in section 2. Also, in the latter we review likely impacts of climate change on plague incidence.

Climate Dependence of the Flea Vectors and Rodent Hosts Top

The plague system is the result of complex interactions between its components, the densities, life cycle, dynamics and geographical distributions all of which are individually influenced by climate variables. Climate variables influence the dynamics of flea vectors and rodent hosts with responses varying considerably among species [7], [8]. Figure 1 illustrates the plague cycle in relation to those climate variables known to be important (namely temperature, humidity and precipitation) to the main plague hosts and vectors.

It is accepted that abundance of rodent fleas is affected by ambient temperature, rainfall, and relative humidity, with warm-moist weather providing a likely explanation for higher flea indices [4], [5]. Indeed, temperature, rainfall, and relative humidity have direct effects on development and survival, as well as the behavior and reproduction of fleas and their populations [9]–[12]. For example, the rate of metamorphosis of Xenopsylla cheopis (as a primary flea of the black rat Rattus rattus, X. cheopisis likely the main vector of plague in foci affecting humans), from egg to adult is regulated by temperature. Fleas are ecto-thermic and hence sensitive to temperature fluctuations; this is enhanced by the fact that all of the immature flea stages occur off host. Flea development rates increase with temperature until they reach a critical value; then the survival of immature stages decreases if high temperatures are combined with low humidity [13]. Temperature and relative humidity impact flea survival [5]: survival is in fact inversely proportional to air saturation deficit at a constant temperature[14]. Flea larvae are susceptible to desiccation [15] and typically acquire water from adult excreta. Survival of immature stages of fleas in rodent burrows is also affected by soil moisture that is partly controlled by outside precipitation [16] even though detrimental moisture losses and temperature swings are reduced by living underground [9]. Conversely, when coupled with a high organic load, excessively wet conditions in rodent burrows (e.g., relative humidity >95%) can promote the growth of destructive fungi that diminish larval and egg survival [5], [17].

Rodent survival and population dynamics are also affected by climate. A direct effect occurs when high intensity rainfall causes flooding of rodent burrows [5] but the effects of precipitation on rodent densities are mostly bottom-up [18]. Indeed, rainfall controls primary production which limits rodent abundances [19]. Reproduction and recruitment periods often follow wet seasons when increases of primary production can be used to build up juvenile populations [20]. Accordingly, rodent population densities show clear association with annual rainfall and its seasonal distribution e.g., in Chile[21]–[23], Tanzania [24], and Australia [25], [26]. But the relation between precipitation patterns and rodent densities can be complex, localized, and dependent on the timing and the intensity of precipitation events (see also below) [8], [27]. Temperature effects on rodent populations are less clear in part because rodents are homeothermic and hence do not respond immediately to changes in ambient temperatures. In temperate areas, low temperatures in winter can nonetheless negatively affect rodent populations either directly or through low food availability [28]. Nevertheless, under some circumstances, conditions detrimental to hosts or vectors can favor the maintenance of plague. Evidence of hibernation as a factor of prolongation or modification of Y. pestis infection in rodents would need further elucidation. The flea Citellophilus tesquorum altaicus for instance, is supposedly able to maintain a plague infection over the winter by feeding on hibernating long-tailed Siberian souslik (Citellus undulatus) [29]. Also, populations of Tatera indica aestivating during adverse conditions in India presumably continue to act as hosts for infected fleas, thereby promoting the persistence of plague infection within the area [30]. Hence, the survival of Y. pestis in relatively plague-resistant burrowing rodents that interrupt their activities to hibernate through winter or aestivate in summer could influence or prevent the transient temporal and spatial extinction of plague occurrence.

Human Plague Incidence Is Not Unrelated to Human Factors

Human activities and behavior in plague-infected areas are also to be considered as important determinants of plague transmission to humans [8]. When occurrences of plague are due to human intrusions in natural plague areas, it is thus important to consider climate as a second order variable that influences disease incidence through human behavior (drought, famine, war, or other events). In Argentina, plague transmission reportedly occurred during the harvesting season [31]. In Lushoto, a plague endemic region in Tanzania, daily and gender activities seem to impact plague levels [32], although plague tends to peak during the season with the least agricultural activity, which is a time when people usually gather in houses.

What Plague Niches Reveal about Plague's Environmental Preferences

Plague foci are present over an expanded geographical range that includes the Western US, portions of South America, East and South Africa, and Southeast Asia [33]. Long-term maintenance of plague in defined ecological niches may inform us about the environmental conditions that are required for plague to establish in permanent foci. Unfortunately, enzootic plague is poorly described; in many foci, local reservoirs have yet to be identified. The geographical limits of plague territories are hence rarely defined or only by occurrence in domestic rodents and humans [34]. It is reasonable to assert that plague manifests itself under various ecological conditions [35], [36]. It is noteworthy though, that modern plague foci in North and East Africa, Western North America, parts of South America, and many scattered regions in Asia (notably China and Kazakhstan) occur primarily in either semi-arid to arid areas or low humidity forest types of habitat, and the disease apparently fails to persist for long periods in humid tropical lowland areas (except from occasional invasion through movement of infected humans or transportation of infected rodents or fleas) [37]–[39]. Also, plague is almost invariably absent from the hottest and driest desert regions like the Sahara or Sonoran deserts [37],[40].

The Complexity Introduced by Interactions among Scales and Other Nonlinearity Top

The previous section reviewed reported effects of climate variables on the components of the plague cycle, indicating that climate affects rodents and fleas individually and their population dynamics and structures. Consequently, climate impacts the natural cycle of plague as a whole and in ways that are not likely to reflect simply the sum of these individual effects. In this section, we review studies on the effects of climate (including the environment) on plague at different spatial levels and occurrences ranging from rodent burrows to areas that form a coherent and apparently self-sustaining system (a single niche or focus), or even to larger regions that could comprise many such systems (several foci). We emphasize the fact that (i) scales relevant to plague ecology are nested within each other, as shown in Figure 2, so that climate effects at a given scale may not be simply extrapolated from those observed at a smaller scale, and (ii) processes exist that prevent the plague system from responding to climate fluctuations in a way that simply reflects the sum of the responses of its individual component.

Figure 2. Illustration of the abiotic environment impact on the plague cycle as a function of spatial scale.

Arrows represent connections affected by climate (see Figure 1 for the meaning of color coding). Most climate variables act over a wide range of scales and only the effects we deemed most important are represented. At the level of individuals, populations and communities hosts and vectors are influenced by climate variability at the relevant scale (local or regional). At the smaller scale, the burrow acts as a filter on climate variables. Note that secondary hosts are placed at the kilometer and larger scale on the basis of the type of information generally available regarding their infection.

doi:10.1371/journal.ppat.1002160.g002

It is readily apparent that associations exist between large-scale climate such as climate indices and plague/plague hosts dynamics; associations that can be consistently explained by processes detailed in the first section. Effects of precipitation patterns on plague incidence are for instance assumed to be the results of climate's bottom-up effects on plague hosts. In Peru, climate fluctuations associated with El Niño were related to a bubonic plague outbreak in 1999 [41]. In northern Colorado, prairie dog colony extinctions attributed to plague were weakly associated with El Niño southern oscillation[42]. In the Western US, spatial synchrony of periods with low and high number of human plague occurrences throughout the west revealed large scale synchrony [43]. In most foci of the southwestern part of this region, above normal precipitation in winter and spring was used to explain increases in human plague cases [44], and high summer temperatures, decreases of its incidence in the same area [45]. The El Niño/Southern Oscillation (ENSO) and the Pacific Decadal Oscillation were similarly related to precipitation, temperatures, food availability, and the number of plague cases themselves [46]. Finally, the increase rate of human plague in China is associated at the province level with the Southern Oscillation Index and Sea Surface Temperature of the tropic Pacific east equator [47]. An important assumption to the above-cited studies is that large-scale climate variability produces coherent and synchronous effects on rodent hosts populations. Few studies actually investigate the reality of the invoked synchronous trophic forcing on plague hosts' population dynamics so as to demonstrate such a climate induced bottom-up control. At this point, it is worth mentioning a counterexample provided by Kausrud et al. [48], who investigated the population dynamics of great gerbils Rhombomys opimus—the main plague host in Kazakhstan—and demonstrated spatial synchrony of their populations over areas larger than the ones expected by migration processes. Their results indicate that the observed synchrony of great gerbil's densities was most probably due to the effects of climate and that similar bottom-up processes could also synchronize plague activity in this focus.

In any case, there are caveats to inferring processes occurring at small scale as a means to explain the ones observed at larger scales. First, causal relations can typically only be suggested (e.g., by a chain of supposedly causal processes from climate indices to relevant climate variables and from these to plague incidence) but not demonstrated. More problematically, a variety of processes can be expected to interfere with each other in the transition from small to large scale. Tentatively, we propose below a classification of these processes into two categories. The first ones pertain to the complexity of the environment itself and the second ones to population interactions.

An example in the first category can be provided by studies showing that rodent burrows could be considered a “climate filter”. Conditions in rodent burrows are subject to environmental factors from nearby surroundings such as temperature, humidity, vegetation, various soil properties (e.g., soil texture and structure, soil organic carbon content, etc.), and other landscape factors (e.g., slope, orientation with respect to dominant winds, sun exposure, etc.). But, the underground location of most burrows implies that conditions inside these structures fluctuate only moderately [49], [50]. In fact, temperatures inside and outside burrow systems are highly correlated, but inside humidity is a complex function of past rainfall and soil characteristics [51] rather than of present ambient humidity[52]. Note that investigations on burrow micro-climate have been conducted in different parts of the world [51], [53], [54], including in plague-endemic regions, but these measurements were generally obtained from only a small number of natural or, in some instances, artificial burrows, allowing investigators to draw only tentative conclusions from the results of these studies [49], [55]. Perhaps more importantly for our present purposes, climate conditions inside the burrows could specifically influence the distribution of plague vectors so that hosts' distribution becomes insufficient to explain vectors distribution, a situation that has been observed in plague areas in Madagascar [56]–[58] or plague-free areas in Israel [59], [60]. These examples emphasize the difficulty of upscaling processes by simple extrapolation. Among the numerous other examples of environment-related complications are the landscape heterogeneities within plague areas. In particular, strong orographic forcings frequent in plague areas locally affect large-scale climate variability [61]. In fact, accurate plague prediction models seem to require high resolution environmental and climate representation (e.g., 250-m resolution images accurately predict plague distribution when 10-km resolution images fails in sub-Saharan Africa). According to the authors, plague focality can not be explained by fragmented environmental conditions at this coarse scale [35], [62].

In the second category are the complications introduced by interactions within and between plague host and plague vector populations in their response to climate variability. It is commonly expected that fluctuations in abundance of rodent hosts, e.g. induced by climate variability, will translate into plague prevalence fluctuations. However, the relationship between host abundance and host prevalence is complex and scale dependent. Field studies of rodent reservoirs show a negative correlation between host abundance and host prevalence at seasonal time scale. The finding has been explained by the juvenile dilution effect, that is, the arrival of numerous healthy juveniles in a population [63]; an effect likely to be relevant for diseases with no vertical transmission such as plague (or Hantavirus [64]). In contrast, a few longer field studies (>5 years) show a positive, although delayed relationship between reservoir abundance and prevalence [63]. These antagonist responses to variability at different time scales are typical of systems in which nonlinear interactions play an essential role. The different responses of rodent and flea populations to climate (fast for fleas while rodents tend to integrate environmental conditions over some years) provide another reason for questioning the existence of a straightforward link between abundance and prevalence. A more complex model was proposed for the Western US, in which human plague incidence depends both on time-lagged precipitation events, which presumably increase rodent numbers and favor plague epizootic, and on relatively cool summer temperatures during the plague transmission season, which are favorable to infectious fleas [45]. This model has been coined “trophic cascade hypothesis,” although it has yet to be tested rigorously for plague under field conditions [65] (see also [66] for a discussion on the accuracy of the use of the term “trophic” for the cascade hypothesis). In particular, the scale at which the trophic cascade model is valid needs to be addressed. Parmenter [44], who first introduced this model, shows its relevance at a local scale (i.e., by demonstrating significant associations between plague and nearby precipitation), but could not extend this result to a state-wide level. Interestingly, a cascade relationship was recovered at an even larger scale by Ben-Ari[46], possibly because the integration of delayed density-dependence effects of large-scale climate on rodents were taken into account at decadal time scales. The study by Stenseth et al. [67] illustrates the challenge that needs to be confronted when addressing cascading effects of climate on plague prevalence in nature. There are numerous relationships between climate elements (temperature and precipitation with or without lags) and various ways these elements can impact the plague components (in this particular case rodent density, prevalence, and flea burden). The type of dataset that would let us isolate/untangle the mechanisms and the spatio-temporal scales at which processes operate may not be available.

These examples do not necessarily invalidate studies that scale up small-scale results (individual measurements, lab experiments, local correlations, etc.) in the simplest way, but we believe they illustrate the need for more investigation on the impact of complex interactions and environment heterogeneities at intermediate scales.

Implications for Climate Change Top

The need to understand disease responses in relation to climate variability is made particularly acute by ongoing global climate change. Effects of temperature rise on vector-borne diseases and notably the ones involving free-living stages of terrestrial animals are expected [68]. Beyond that, a lot of uncertainty remains on whether or how climate change might affect pathogens and disease transmission, i.e., changes in population size (for vectors or hosts), overall prevalence, timing and seasonality, or shifts in geographical distribution. There are various choices to be made when addressing climate change impact on a disease like plague, particularly with respect to the degree of complexity that should be chosen for climate models and any associated biological models and the relation between them.

Stenseth et al. [67] performed a sensitivity study to a one-degree increase in temperature into a statistical host vector plague model developed specifically for Kazakhstan. They show that this (simple) climate change scenario would lead to a 50% increase in plague prevalence among great gerbils. Nakazawa et al. [69] used two Global Circulation Models (GCMs) to infer mean temperature and precipitation changes between the present and a 30-year period centered around 2055. These changes were then applied to a higher resolution present state GCM that provided a climate changed forcing state, which was fed into an Ecological Niche Model (ENM) predicting plague occurrences in the US from a set of environmental variables. They show subtle shifts of plague habitats (generally northward). Snall et al. [70] used an elaborate procedure to downscale climate scenarios from several GCMs before using these data to force an explicit model for the joint host-parasite dynamics of black-tailed prairie dogs and plague in the Western US. A related decrease in the number of infected prairie dog colonies (leading to an increase in prairie dog colonies) is predicted, presumably, as a consequence of the negative impact of increased frequency of abnormally hot days on plague transmission.

These studies are difficult to compare with each other because of the specificities of their methodologies even when they lead to contrasting results over the same region [70]. Admittedly, more investigations are required. Among the numerous possible approaches, the safest arguably would rely on using climate-forcing sensitivities of intermediate complexity where biological models are forced by existing modes of climate variability. This makes sense not only because climate change will in large part occur through a modification of these modes (which can be extracted from Intergovernmental Panel on Climate Change [IPCC] GCMs [61]), but also because biological data are then available for evaluation.

Conclusion Top

Climate impacts all components of the plague cycle (host, vector, and pathogen) in various ways and over a wide range of scales (from micro—individual flea life cycle—to macro—a plague area composed of several disjoint foci). Several studies have established links between plague occurrence and climate factors that can a posteriori be justified by assuming the validity at a large scale of relationships that have only been observed at a small scale (assumption of linearity). We have reviewed both the successes and the limitations of this assumption. To go beyond simple inferences on how climate fluctuations (including long-term climate change) affect plague, it might be necessary to select a (or a few) preferential scale, on the basis of the fact that they would be the most informative and/or relevant for public health policies. In this regard, intrinsic dynamics of plague hosts and vectors should be kept in mind as it alone greatly contributes to the entanglement of scales that drive the overall dynamics of plague prevalence [71]. Further, assessing plague risks for humans at such scales may in fact require investigating plague dynamics on a much wider range of scales and presumably include a fuller description of the plague system in its environment, as we have tried to outline in this review.

Acknowledgments Top

We thank Ulf Buentgen for his help with figure preparation; Mike Begon, Ulf Buentgen, and Sasha Gershunov for discussions on plague and climate; and Xavier Capet for numerous comments and corrections on earlier versions of the manuscript. We also thank two anonymous reviewers for providing helpful comments to an earlier version of this contribution.

Author Contributions Top

Conceived and designed the experiments: TBA NCS. Performed the experiments: TBA SN. Analyzed the data: TBA SN. Wrote the paper: TBA SN KLG KK AL HL NCS.

References Top

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