After several months of waiting, the sequencing run of 20 strains of our favorite species has finally been completed. There were several delays, mostly due to the upgrade of my collaborator's SOLiD sequencer to version 4. In addition there were problems with the emulsion PCR, also due to upgrades. Anyway, in the end it appears we have very good, paired-end sequence data. Preliminary analysis of one of the barcodes suggests we have about 80+% of the reads mapping to the reference genome, with extremely good coverage, about 150x.
Assembly of the 20 strains will commence next week. Then the fun begins, at least for my post doc!
Tuesday, May 10, 2011
Thursday, August 19, 2010
We are often collateral damage
In a recent post, Ed Yong (Not Exactly Rocket Science) describes the concept of "coincidental evolution" of certain bacterial species that are virulent in people.
He discusses several examples of species that appear to have evolved mechanisms to defend against or escape natural predators in their environmental niche.These predators include amoebas (Escherichia coli, Legionella pneumophila), where resistance to grazing or the ability to survive engulfment allows the bacteria to do the same thing with regards to macrophages in a human host. Another example is when normally harmless Streptococcus pneumoniae becomes infectious for humans after it is exposed to Haemophilus influenzae; evidently this exposure induces the former to produce a thicker capsule that makes the bacterium resistant to the human immune system.
I've thought about this concept of "accidental virulence" for quite some time. One of the pathogens I work on, Vibrio parahaemolyticus, forms an extremely diverse species, with a highly plastic genome. This variability can be explained in part by the large number of mobile genetic elements and bacteriophage remnants, as well as the ability to take up and incorporate exogenous DNA by transduction, conjugation, and transformation. Yet when isolates from clinical infections are examined by methods such as multilocus sequence typing, these 'by definition' virulent strains appear to be part of a small number of highly clonal complexes. The normal environmental niche of these bacteria is in estuarine marine waters, where they are found free swimming or colonizing a variety of biotic (copepods, zooplankton, phytoplankton, shellfish) and biotic (anything with chitin) surfaces.
For years virulence of this and related species have been studied by classical molecular pathogenesis methods, i.e., find a suspect virulence gene, knock it out, and look at changes in the mutant's ability to do something to an experimental host, tissue cell line, etc. Yet in my opinion none of these studies have developed a method to truly say that a given strain will be virulent and highly capable of causing disease. These are opportunistic pathogens, so it seems to make sense that the few strains capable of infecting and causing pathology in humans have actually developed or adapted new ways to survive and/or proliferate in their environment, perhaps in response to changes in local environmental factors. It just so happens that these adaptive changes make them more virulent, maybe increased survival in stomach acid, enhanced colonization of the gut epithelium, or secretion of extracellular enzymes or toxins we don't yet know about.
All reasons why I'm very anxious about getting my genome sequencing project off the ground!
If you’re trapped in a building, it’s probably not the best time to start setting fire to things. But this is exactly what some bacteria do when they find themselves in a human; they cause diseases that are potentially fatal but not contagious. Without an escape, they risk going down with their host. This seems like a ludicrous strategy but we’re looking at it from the wrong perspective – our own. In truth, humans often have nothing to do with the diseases that plague us; we’re just collateral damage in an invisible war.
Like all living things, bacteria have to defend themselves against predators like amoebas. Some species do so using resistance genes that turn them from passive victims into aggressive fighters. And by coincidence, these same adaptations make them more virulent (good at causing disease) in human bodies. We’re just caught in the crossfire."
(From "Disease by coincidence – why we’re caught in the crossfire of a hidden war" | Not Exactly Rocket Science | Ed Yong | Discover Magazine)
He discusses several examples of species that appear to have evolved mechanisms to defend against or escape natural predators in their environmental niche.These predators include amoebas (Escherichia coli, Legionella pneumophila), where resistance to grazing or the ability to survive engulfment allows the bacteria to do the same thing with regards to macrophages in a human host. Another example is when normally harmless Streptococcus pneumoniae becomes infectious for humans after it is exposed to Haemophilus influenzae; evidently this exposure induces the former to produce a thicker capsule that makes the bacterium resistant to the human immune system.
I've thought about this concept of "accidental virulence" for quite some time. One of the pathogens I work on, Vibrio parahaemolyticus, forms an extremely diverse species, with a highly plastic genome. This variability can be explained in part by the large number of mobile genetic elements and bacteriophage remnants, as well as the ability to take up and incorporate exogenous DNA by transduction, conjugation, and transformation. Yet when isolates from clinical infections are examined by methods such as multilocus sequence typing, these 'by definition' virulent strains appear to be part of a small number of highly clonal complexes. The normal environmental niche of these bacteria is in estuarine marine waters, where they are found free swimming or colonizing a variety of biotic (copepods, zooplankton, phytoplankton, shellfish) and biotic (anything with chitin) surfaces.
For years virulence of this and related species have been studied by classical molecular pathogenesis methods, i.e., find a suspect virulence gene, knock it out, and look at changes in the mutant's ability to do something to an experimental host, tissue cell line, etc. Yet in my opinion none of these studies have developed a method to truly say that a given strain will be virulent and highly capable of causing disease. These are opportunistic pathogens, so it seems to make sense that the few strains capable of infecting and causing pathology in humans have actually developed or adapted new ways to survive and/or proliferate in their environment, perhaps in response to changes in local environmental factors. It just so happens that these adaptive changes make them more virulent, maybe increased survival in stomach acid, enhanced colonization of the gut epithelium, or secretion of extracellular enzymes or toxins we don't yet know about.
All reasons why I'm very anxious about getting my genome sequencing project off the ground!
Sunday, May 23, 2010
Genomics here we come
It's been a very busy first 6 months of 2010, with much of my time focused on doing "other" things critical for my job, and to the center/agency programs. Unfortunately these time consuming activities have considerably slowed my ability to push some of the lab science forward. It didn't help that the post doc I had who was working on the genomics project left to take an internship with another government agency. This was good for him and important for his future aspirations, it paid him considerably more, and I felt I really had to encourage him to take it. But it sure caused a loss of momentum, and with the time commitment needed for his internship, I don't see him writing up one of his two projects unless I try to draft it.
However, unless I am requested to provide research support for a microbial perspective on seafood safety or ecological damage assessments as a result of the Gulf of Mexico Transoceanic oil spill disaster, things should start heating up this summer. I have a new post doc coming in July who will drive the genomics work. A couple of months ago he spent 4 weeks in the lab on an internship (funded through one of the national programs that my program is a part of), and I was both impressed and relieved that he will prove to be one of the better ones.
Everything's in place, financially and organizationally, to have 10-16 strains of my favorite bacterial species sequenced to ~100x coverage on a SOLiD next gen sequencer (when do they become current gen?). Strains to be sequenced have already been subjected to MLST analysis, clonal groups characterized and relationships established. The objectives include determining what is different at the genome level between clinical (therefore virulent) strains, which form one tight clonal complex and appear rare in the environment, and other environmental isolates that belong to other phylogenetic groups and are not isolated from clinical cases.
This should be fun, and I do need some of that at work!
However, unless I am requested to provide research support for a microbial perspective on seafood safety or ecological damage assessments as a result of the Gulf of Mexico Transoceanic oil spill disaster, things should start heating up this summer. I have a new post doc coming in July who will drive the genomics work. A couple of months ago he spent 4 weeks in the lab on an internship (funded through one of the national programs that my program is a part of), and I was both impressed and relieved that he will prove to be one of the better ones.
Everything's in place, financially and organizationally, to have 10-16 strains of my favorite bacterial species sequenced to ~100x coverage on a SOLiD next gen sequencer (when do they become current gen?). Strains to be sequenced have already been subjected to MLST analysis, clonal groups characterized and relationships established. The objectives include determining what is different at the genome level between clinical (therefore virulent) strains, which form one tight clonal complex and appear rare in the environment, and other environmental isolates that belong to other phylogenetic groups and are not isolated from clinical cases.
This should be fun, and I do need some of that at work!
...staying put
It's been a long time since I last wrote here, and I just realized I never did post the outcome of my candidacy for a marine genomics faculty position (discussed earlier here).
Obviously, it wasn't me who was selected. I probably would have written about that. After almost 10 months of waiting, the med school dean/committee picked a very accomplished researcher, big research group, Howard Hughes Professor, ~250 publications, yada, yada. Really, I was flattered to be recruited to apply, and then asked to interview; then to make it as a top 3 candidate was icing on the cake. But from what what I know about the person selected, and what I've heard from others associated with both the university and the government lab where the person's research group will be based, it was kind of a strange selection. His background and career, while stellar, did not really fit the requirements and qualifications that were originally advertised. I'm not trying to sound bitter, because I'm not, and I realize shifts in positions happen. I've also heard that restructuring at the school might have made it less attractive to make the jump for someone like me.
So, as far as I know, I'm not going anywhere. I have several good years left, so I'm finally acting on some opportunities to make some changes in my work situation, plus I'm now more determined to follow through on many of the goals for the research I've set.
Obviously, it wasn't me who was selected. I probably would have written about that. After almost 10 months of waiting, the med school dean/committee picked a very accomplished researcher, big research group, Howard Hughes Professor, ~250 publications, yada, yada. Really, I was flattered to be recruited to apply, and then asked to interview; then to make it as a top 3 candidate was icing on the cake. But from what what I know about the person selected, and what I've heard from others associated with both the university and the government lab where the person's research group will be based, it was kind of a strange selection. His background and career, while stellar, did not really fit the requirements and qualifications that were originally advertised. I'm not trying to sound bitter, because I'm not, and I realize shifts in positions happen. I've also heard that restructuring at the school might have made it less attractive to make the jump for someone like me.
So, as far as I know, I'm not going anywhere. I have several good years left, so I'm finally acting on some opportunities to make some changes in my work situation, plus I'm now more determined to follow through on many of the goals for the research I've set.
Friday, November 6, 2009
One Health
A few months ago I was asked to write a paragraph describing the One Health Paradigm for a regional white paper on the regional marine ecosystem. This is what I came up with, heavily borrowing from several sources. It has become a useful way for me to describe the the multifaceted approach I'm moving my lab's research toward. Specifically, an approach that includes the role of environmental factors (abiotic and biotic), human factors (health status, habits, etc.), and pathogen genetic factors, in order to understand why only a small number of strains of a given species of a marine bacterium are truly virulent.
Someone (and I can't remember who and where) used this image to describe how changing migration patterns of animals and humans contribute to new infectious disease spread.
Comments welcomed.
The One Health Paradigm reflects the inter-relationships between environmental, animal, and human health. The One Health Approach for improving human health is equally applicable to terrestrial and aquatic environments. Of the 1,461 infectious diseases now recognized in humans, approximately 60% are due to multi-host pathogens characterized by their movement across species lines. Over half of all new or emerging infectious diseases since the 1940s have jumped from domestic and wild animals to humans, and it is fully expected that this trend will continue. Anthropozoonoses, diseases that effect both animals and humans, often result in animals serving as reservoirs for re-emerging or new diseases. Environmental degradation through pollution and contamination, or changes in the environment brought about by climate change, may result in favorable settings for expansion of existing infectious diseases, may increase the transmissibility of these diseases, or may lead to altered patterns of pathogen virulence as they rapidly adapt to new environmental cues. Animal and human migration patterns also shift in response to climate change, further leading to new routes of exposure. Therefore, to fully understand, forecast, and control emerging infectious diseases requires an interdisciplinary and holistic approach that combines the studies of pathogens and their virulence, animal health and zoonoses, and the role of climate change and other factors on environmental health. While the One Health approach is often used in context for the control of infectious disease, the paradigm is easily extended to include an understanding of the fate of contamination of the environment with a variety of chemicals, fertilizers, and antibiotics. These anthropogenic factors have both direct and indirect impacts on human health. In all cases, the One Health approach is aided by the incorporation of the concept of sentinel species, including the acquisition of pathogens infectious to humans as well as the impacts of chemical contaminants on development, reproduction, and overall health.
References:
King, L. (Ed). One Health: A New Professional Imperative. One Health Initiative Task Force, American Veterinary Medical Association (2008) pp. 1-76
King, D. A., C. Peckham, J. K. Waage, J. Brownlie, and M. E. J. Woolhouse. Infectious diseases: preparing for the future. Science (2006) vol. 313 (5792) pp. 1392-3
Torrey E. F., and Yolken R. H. Beasts of the Earth. New Brunswick, NJ: Rutgers University Press (2005).
other
2009 ASM General Meeting symposium description: "One Health - A New Paradigm for Microbiology and Public Health" (May 19, 2009)
MicrobeWorld (video of ASM press conference for same symposium)
Someone (and I can't remember who and where) used this image to describe how changing migration patterns of animals and humans contribute to new infectious disease spread.
Comments welcomed.
Tuesday, October 20, 2009
Flu vaccination
A few days ago I got vaccinated against the flu for the first time in my life. This was the "regular" type A seasonal influenza vaccine, not H1:N1. Turns out, at least with my health insurance cooperative, that at my age I don't fall into the necessary risk category for H1:N1. This is between 6 and 25 or over 60 years old, or those at risk because of other predisposing health conditions.
So why haven't I been vaccinated in the past? I think it stems from one of my early microbiology classes as an undergraduate, during the 1976 swine flu epidemic. Shortly after mass vaccination started, there were reports of Guillain-Barre syndrome affecting a small fraction of those vaccinated (~4000 out of 46 million vaccinated, or 0.01%; "Reflections on the 1976 Swine Flu Vaccination Program"). In spite of the low risk, a professor teaching a virology class I was taking (a well respected virologist) suggested that the vaccine may not have been quite ready for mass immunization, and that was enough to dissuade me.
So even though I've been an active researcher in infectious disease and completely understand the risk/benefits of vaccination, until this week I resisted the flu vaccine. I've had just about every other recommended one and never blinked, and darn well made sure my kids had all of theirs. In fact it drives me crazy when i hear the myriad excuses people make for not getting their kids vaccinated for measles, pertussis, and other highly communicable infectious agents. Maybe I resisted because I think I've only had "real" influenza a few times in my life. Or maybe it's my faith in "herd immunity." However after seeing enough reports that HI:N1 appears to be especially hard on otherwise health young people, I called both of my kids (19 and 23) and made them promise to go get it. I'll be on their backs until they do. And I'll be getting annual flu shots myself from now on.
So why haven't I been vaccinated in the past? I think it stems from one of my early microbiology classes as an undergraduate, during the 1976 swine flu epidemic. Shortly after mass vaccination started, there were reports of Guillain-Barre syndrome affecting a small fraction of those vaccinated (~4000 out of 46 million vaccinated, or 0.01%; "Reflections on the 1976 Swine Flu Vaccination Program"). In spite of the low risk, a professor teaching a virology class I was taking (a well respected virologist) suggested that the vaccine may not have been quite ready for mass immunization, and that was enough to dissuade me.
So even though I've been an active researcher in infectious disease and completely understand the risk/benefits of vaccination, until this week I resisted the flu vaccine. I've had just about every other recommended one and never blinked, and darn well made sure my kids had all of theirs. In fact it drives me crazy when i hear the myriad excuses people make for not getting their kids vaccinated for measles, pertussis, and other highly communicable infectious agents. Maybe I resisted because I think I've only had "real" influenza a few times in my life. Or maybe it's my faith in "herd immunity." However after seeing enough reports that HI:N1 appears to be especially hard on otherwise health young people, I called both of my kids (19 and 23) and made them promise to go get it. I'll be on their backs until they do. And I'll be getting annual flu shots myself from now on.
Wednesday, June 10, 2009
Research change of direction
Lately, for a variety of reasons, I've been moving much of the lab research away from single gene pathogenesis studies towards the application of bacterial genomics and metagenomics to studies of microbial ecology and adaptation to the environment. Of particular interest is to examine whether environmental (climate) change may be driving adaptation and selection of the microbial community, with a focus on adaptation that leads to increased virulence of specific pathogens. We are using a variety of genetic, genomic, and phylogenetic tools for this now, and soon we will be applying comparative whole genome strategies to get at the questions we want to answer. The overall goal is to develop better sensors, forecasting tools, or add additional data to risk models that can be used to improve human health (prevention of infectious disease) or as measurements of environmental health.
Over the years I've occasionally had trouble fitting my laboratory's microbiology research into the main research and resource management focus of my immediate line office. Overall, this newer direction now fits in well with the mission of my agency, in that the results of the basic research can be more easily shown to have direct applicability to products that should benefit resource and public health managers. (Some other time I may write about ecosystem services.)
This direction has necessitated some self 're-training' in the disciplines of genomics and bioinformatics, although I've been moving into this arena for some time now (recent publication). The challenge is stimulating and energizing, something I think many of us need time to time in this profession. I'm eager to get going.
Over the years I've occasionally had trouble fitting my laboratory's microbiology research into the main research and resource management focus of my immediate line office. Overall, this newer direction now fits in well with the mission of my agency, in that the results of the basic research can be more easily shown to have direct applicability to products that should benefit resource and public health managers. (Some other time I may write about ecosystem services.)
This direction has necessitated some self 're-training' in the disciplines of genomics and bioinformatics, although I've been moving into this arena for some time now (recent publication). The challenge is stimulating and energizing, something I think many of us need time to time in this profession. I'm eager to get going.
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