Take Advantage of These ASM Resources


Step 1: Register for ASM Microbe 2017

Join your peers from around the world to explore the complete scope of microbiology – from basic science to translational and clinical application – at ASM Microbe 2017 (June 1–5, 2017, New Orleans, Louisiana). The special Infectious Diseases Fellows Program offers an opportunity for you to attend the meeting free of charge.

>> View the program.

>> Register before April 20 for the special rates.


Step 2: Listen to the ASM-CLSI Webinar Series

Register for the ASM-CLSI Webinar Series in Antimicrobial Susceptibility Testing: Fundamentals of Susceptibility Testing, Reporting, and Test Validation to learn the fundamentals for AST in the clinical microbiology laboratory. Registration includes access to the live webinars, the recorded presentation, and P.A.C.E.® or Florida continuing education credits.

>> Register for the webinar now.





Step 3: Join ASM

Join the world’s largest life science society that works for you.  Enrich your network with ASM’s clinical microbiology listserv, pursue career opportunities with ASM’s career website, and obtain discounts* on public health-related books, journals, and conferences!  Membership starts at $22. 

>> Become an ASM member now.

* Discounts do not apply to all membership categories.

mSphereDirect Sign Up

mSphereDirect Sign Up



Image Gallery



Contaminated Gloves Increase Risks of Cross-Transmission of Healthcare-Associated Pathogens
Dr. Kazue Fujita










legionella strains

Ongoing Monitoring of Legionella in Flint in the Wake of the Drinking Water Crisis
Dr. Otto Schwake

Eight strains of Legionella isolated from a health care center in Flint, MI during March 2016.  Photograph: Otto Schwake









water bottlesSamples of discolored tap water and a rusty water filter provided by Flint residents.
Photograph: Virgina Tech/Jim Stroup















S.mutans colony morphology

Sharing of Tooth Decay Causing Bacterium Among Children and Their Families
Stephanie Momeni

S. mutans colony morphology











SEM.K904 on Bleb.pseudo.copyResearch Shows New Mechanism That Can Cause Eye Inflammation
Dr. Robert Shanks

Pseudo-colored electron micrograph of Serratia marcescens bacteria (red) on a human corneal cell in vitro.  The yellow arrow indicates a large surface bleb induced by a toxin produced by the bacteria.  The white bar indicates 10 microns.









A Novel Therapy for Genital Herpes Engages Immune Cells to Provide Significant Patient Benefits for at Least a Year
Dr. Kenneth Fife, MD, PhD, investigator and Professor of Medicine at Indiana University



























Pisciotta1Photo: WCU Researchers: From left to right. Dr. John Pisciotta, graduate student Paige Minka and undergraduate Jeremy Irving prepare to install sMFCs in Paradise Farms pond (Downingtown, PA).
















muddy microbesFig. 1:  sMFC components and experimental installation plan depict two sMFCs with identical sediment-buried graphite anodes wired (in red) to transmit microbially-generated electric current from anodes to an upper cellular data relay unit (upper box) that transmits the data from the field site. Electrons then pass via wires (green) to carbon cloth cathodes (grey ovals) suspended in the water at variable depths. Leftmost sMFC features a surface cathode while the sMFC at right has a submerged cathode. Identical replicate sMFCs (not shown) were included in the study.

mSphere Direct





Thank you for your RSVP

Thank you for your RSVP to the ASM Officers' Reception.


Saturday, June 18th from 7:30 pm to 9:00 pm

The Westin Boston Waterfront

Grand Ballrooms BCDE (Concourse Level)

425 Summer Street

Boston, MA

Membership for Clinical Microbiologists



“Who is looking out for the interests of clinical microbiologists? In my view, the American Society for Microbiology is doing this exceedingly well.”

Joseph Campos, PhD, D(ABMM), FAAM
Director of the Microbiology Laboratory at Children’s National Medical Center

ASM understands the vital importance clinical microbiology plays in sustaining the health of the world population. We know the daily challenges that you face in the prevention, diagnosis, and treatment of infectious disease. ASM supports the clinical microbiological community in many unique ways – with cutting-edge information, professional certification and awards, and a robust advocacy for the field. Here is how we can help you…

Access to cutting-edge information through:

  • ASM’s Microbe 2017 meeting, combining the dedicated clinical track of the former General Meeting with the premier infectious disease offerings of ICAAC
  • ASM Journals – seven journals devoted to clinical microbiology and immunology that delivers authoritative and high-quality clinical research
  • CUMITECH lab references – now free with membership!
  • Clinical Microbiology Portal – access to a database of over 1,500 expertly answered questions, and more
  • Two vibrant listservs dedicated to current clinical issues
  • NEW MEMBER TYPE:  CLS/MT/MLT Labtech Membership with up to 12 CE credits


Certify your accomplishment and expertise through:

  • Certification by the American Board of Medical Microbiology (ABMM), the American Board of Medical Laboratory Immunology (ABMLI), and the National Registry of Certified Microbiologists (NRCM)
  • ASM’s Continuing Education (CE) Portal – the online source for accessing and tracking all continuing education activities
  • Awards and recognition specifi cally focused on clinical microbiologists including the BD Award for Research in Clinical Microbiology, Scherago-Rubin Award, and the Beckman-Coulter Young Investigator Award

Advocacy for the interests of the clinical community through:

  • Encouraging the adoption of sound policies
  • Monitoring federal legislation and regulation
  • Communicating microbiological issues to the public
  • Participating in CDC/APHL organized meetings


Thank you for your RSVP

Thank you for your RSVP to the Division Officers Forum.

The meeting will be held on Thursday, June 16th from 8:30 - noon at
The Westin Boston Waterfront
Grand Ballrooms C
425 Summer Street
Boston, MA

A continental breakfast will be served.

Clinical Microbiologists

“Who is looking out for the interests of clinical microbiologists? In my view, the American Society for Microbiology is doing this exceedingly well.”

Joseph Campos, PhD, D(ABMM), FAAM
Director of the Microbiology Laboratory at Children’s National Medical Center

ASM understands the vital importance clinical microbiology plays in sustaining the health of the
world population. We know the daily challenges that you face in the prevention, diagnosis, and
treatment of infectious disease. ASM supports the clinical microbiological community in many
unique ways – with cutting-edge information, professional certifi cation and awards, and a robust advocacy for the field. Here is how we can help you…

Access to cutting-edge information through:
• ASM’s Microbe 2017 meeting, combining the dedicated clinical track of the former General Meeting with the premier infectious disease offerings of ICAAC
• ASM Journals – seven journals devoted to clinical microbiology and immunology that delivers authoritative and high-quality clinical research
• CUMITECH lab references – now free with membership!
• Clinical Microbiology Portal – access to a database of over 1,500 expertly answered questions, and more
• Two vibrant listservs dedicated to current clinical issues
•  NEW MEMBER TYPE:  CLS/MT/MLT Labtech Membership with up to 12 CE credits

Certify your accomplishment and expertise through:
• Certifi cation by the American Board of Medical Microbiology (ABMM), the American Board of Medical Laboratory Immunology (ABMLI), and the National Registry of Certifi ed Microbiologists (NRCM)
• ASM’s Continuing Education (CE) Portal – the online source for accessing and tracking all continuing education activities
• Awards and recognition specifi cally focused on clinical microbiologists including the BD Award for Research in Clinical Microbiology, Scherago-Rubin Award, and the Beckman-Coulter Young Investigator Award

Advocacy for the interests of the clinical community through:
• Encouraging the adoption of sound policies
• Monitoring federal legislation and regulation
• Communicating microbiological issues to the public
• Participating in CDC/APHL organized meetings


Maldi-Tof Webinars

Restricted content

A password is required to access this content.

Multisociety Transition Letter

November 23, 2016

Mr. Donald Trump
Office of President-Elect
1800 F Street, NW
Washington, DC 20006

Dear President-elect Trump:

On behalf of the U.S. scientific, engineering, and higher education community we are looking forward to working with you, as 45th President of the United States, and your administration.

As President you will face a wide range of domestic and international challenges, from protecting national and energy security, to ensuring U.S. economic competitiveness, curing diseases, and responding to natural disasters. These challenges share one thing in common: the need for scientific knowledge and technological expertise to address them successfully.

For this reason, we urge that you quickly appoint a science advisor with the title of Assistant to the President for Science and Technology who is a nationally respected leader with the appropriate engineering, scientific, management and policy skills necessary for this critically important role. This senior level advisor can assist you in determining effective ways to use science and technology to address major national challenges. Moreover, this individual can coordinate relevant science and technology policy and personnel decisions within the executive branch of government.

The economic benefits of advancements in science, technology and innovation have been well documented, estimated by leading economists to have accounted for approximately half of U.S. economic growth over the last fifty years. Past government investments in the U.S. scientific and technological enterprise have fueled our economy, created new jobs, and ensured our global competitiveness and national security. At the same time, these investments have enabled the development of a system of U.S. research universities and national laboratories unmatched in the world.

We know that one of your top priorities will be to focus on ensuring that the U.S. economy remains strong and continues to grow. If we are to maintain America’s global leadership, and respond to the economic and security challenges currently facing the nation, we must build on our strong history of federal support for innovation, entrepreneurship and science and technology.

Toward that end we would appreciate the opportunity to meet with you or leaders of your transition team to discuss how the science and engineering community can assist with developing a path forward to ensure that the U.S. innovation infrastructure grows and flourishes under your administration and to suggest candidates for top science and technology posts.

Thank you for your consideration and we look forward to your response. You may contact Joanne Carney (jcarney@aaas.org) with the American Association for the Advancement of Science (AAAS) to coordinate a convenient meeting time, and we will follow up with a proposed list of attendees.

Rush D. Holt
Chief Executive Officer
American Association for the Advancement of Science

Kevin B. Marvel
Executive Officer
American Astronomical Society

Donna J. Nelson
American Chemical Society

Chris McEntee
Executive Director and CEO
American Geophysical Union

Milan P. Yager
Executive Director
American Institute for Medical and Biological Engineering

Robert G.W. Brown
Chief Executive Officer
American Institute of Physics

Kate P. Kirby
Chief Executive Officer
American Physical Society

Martin Frank
Executive Director
American Physiological Society

Stefano Bertuzzi
Chief Executive Officer
American Society for Microbiology (ASM)

Crispin Taylor
Chief Executive Officer
American Society of Plant Biologists

Nancy Kidd
Executive Officer
American Sociological Association

Robert H. Rich
Executive Director
Arctic Research Consortium of the United States (ARCUS)

Thomas G. Loughlin
Executive Director

Sarah Brookhart
Executive Director
Association for Psychological Science

Mary Sue Coleman
Association of American Universities

Peter McPherson
Association of Public and Land-grant Universities

Keith Yamamoto
Coalition for the Life Sciences

RADM Jonathan White (ret., USN)
President and CEO
Consortium for Ocean Leadership

Wendy A. Naus
Executive Director
Consortium of Social Science Associations

Madeleine Jacobs
President and CEO
Council of Scientific Society Presidents

David M. Lodge
Ecological Society of America

Howard H. Garrison
Deputy Executive Director for Policy
Federation of American Societies for Experimental Biology

Shirley M. Tilghman
Rescuing Biomedical Research

Mary Woolley

John C. Nemeth.
Executive Director and CEO
SIGMA Xi, The Scientific Research Society

Thomas Grumbly
SoAR Foundation

Marty Saggese
Executive Director
Society for Neuroscience

Peter Walter
The American Society for Cell Biology

Elizabeth A. Rogan
Chief Executive Officer
The Optical Society (OSA)


Register for ASMCUE by May 16 and Save $100!

Stop what you're doing right now and take advantage of our Early Registration prices!  Receive discounted rates to attend ASMCUE, including special registration rate for Grad Students and Postdocs. While registering, attendees have the option to support a colleague’s attendance to the conference by making a donation to the ASMCUE travel grant fund. Fees will increase after May 16.

Register here: http://bit.ly/asmcueearlyregwn

Volunteer and Governance Engagement Program Coordinator

The American Society for Microbiology (ASM), headquartered in Washington, DC, is seeking a full-time Volunteer and Governance Engagement Program Coordinator in the Office of the Executive Director department. The incumbent will be responsible for volunteer leadership and governance support, organizational governance nomination, appointments, and recruitment activities and coordinating the annual election of volunteer leadership positions for the Office of the Executive Director. In addition, the incumbent will be responsible for preparing and tracking budget for the volunteer leadership and governance activities.

Premium +1

For a limited time, the first 400 members who renew at the Premium member rate will be given one free membership* to award to the student, postdoc, or colleague of their choice. Hurry and renew!  The offer is only good for the first 400 members who renew, and all must be received by October 15, 2016.


1)  You renew your membership at the Premium level before 10/15/16.

2)   Within 2 business days of processing your renewal you will receive an email with an application attached. 

3)  You select your recipient and forward the application for them to complete and return to ASM.  Please note:  all awarded membership applications must be received by November 15, 2016.


-*Only Student, Postdoc, or Supporting memberships are included in this offer.
- Recipients cannot have been a member during 2016.
- The offer is first-come, first-served: when 400 applications have been awarded the offer will conclude.
- Each Premium member is eligible to receive only one free membership.
- The free membership cannot be used in combination with any other ASM product to receive a discount, or as part of a Lab & Classroom group.
- If are a 2016 Contributing Member and would like to upgrade to Premium in order to take advantage of this offer, either change your member type on the renewal form, and enter $132 for  payment OR select Premium membership when renewing online at www.asmscience.org/renew.

Questions?  Contact membership@asmusa.org



ASM Branches Listening Tour

ASM Branches Listening Tour

Dear ASM Branch member,

I'm on my way to see you. During 2016, I will be on the road for the first ever listening tour of the ASM Branches. I intend to visit in person all 36 ASM Branches in the United States. Actually I've already started. On the first weekend in April, I set out on the first of what will be a series of mostly weekend flying visits, dropping in on ASM Branches and meeting the members in their natural professional habitats.

When I became CEO of the ASM in January, I resolved to test what has been one of my core principles-I was going to listen to ASM members. Visiting all 47,000 ASM members at home seemed a little ambitious, but visiting all 35 branches could give me an incredible overview of part of the organization that is vital to our collective community. I know that once you have visited one ASM Branch, you have seen only that one branch, because they are as diverse as microbial sciences are. So I plan to see all 36 branches.

I want to hear firsthand what the branches need, what they cannot easily find elsewhere, and what they hope ASM Central can do for them. I also want to share the vision for the future of ASM as an organization and to communicate directly about the changes already underway at Headquarters and what changes are to come. It is also a great opportunity for making new friends and having a good time together.

feedbakEqually important to me is the chance to forge personal relationships with so many working microbiologists. During my first two visits, at the Indiana and Rio Grande Branches, I heard exciting stories of scientific discovery and of professional growth. For example, I met Indiana University SouthEast senior Tyler Mercer who is looking for ways to stay in the lab after he graduates. Tyler has become mesmerized by phages and by science in general, but he comes from a family background where there was not much support for studying science. It occurred to me that ASM has made a crucial difference for Tyler. Not only did ASM members show Tyler ways to pursue microbial science, but the very existence of the Indiana ASM Branch reassured him that there are other people who care a great deal about phages and that these people make a good living and have a great career by putting their curiosity and knowledge to work. I left Fort Wayne thinking that this is exactly why we are in business as an association. We are here to make members better off because of their involvement with ASM.

So the ASM Branches listening tour is off to a flying start. On this page you can see my future itinerary and stops so far. I will also post simple videos and photos I take during my visits. Stay tuned, and feel free to connect. As I will tweet about my Branch visits, follow me on Twitter @sutefune or just email me ceo@asmusa.org. If your ASM Branch is not yet on my schedule, feel free to reach out so that we can meet!

Onward and forward, ASM Branches!




April 1-2, 2016 Indiana Branch ASM Meeting April 2016
April 1-2, 2016
Rio Grande Branch ASM Meeting April 2016
April 9, 2016 -
 Rocky Mountain Branch ASM 2016 Spring Meeting
April 14, 2016
Washington DC Branch ASM Joint Meeting with George Mason University Student Chapter ASM April 2016
April 20 2016 -
Northeast Branch ASM Spring Meeting
April 22-23, 2016
Michigan Branch ASM 2016 Spring Meeting
April 23, 2016 - 
Intermountain Branch ASM 2016 Meeting 
April 25, 2016
- Eastern Pennsylvania Branch
April 29, 2016
- Virginia Branch
May 10-11, 2016
Illinois Branch ASM (IL Society For Microbiology) 2016 Spring Meeting 
May 26, 2016
- Puerto Rico Branch
October 27-29, 2016
Southern California Branch 80th Annual Meeting


Indiana Branch - Fort Wayne, IN

Tim Donohue
ASM Past President Tim Donohue
John McKillip
John McKillip speaks about science education
Ellen Wagner
Ellen Wagner, Ball State University
Tanya Soule
Tanya Soule organizer of the ASM Indiana Branch meeting
Tyler Ulysses Mercer
Tyler Ulysses Mercer

Rio Grande Branch - El Paso, TX

Charles Spencer
Dr. Charles Spencer, President of the ASM Rio Grande Branch



Rocky Mountain Branch






Anne Spain
Anne Spain, President of the ASM Michigan Branch
Susan Dunn
Susan Dunn, Dean of Davenport University, host of the spring Michigan Branch meeting



Justin Nielsen and Luke Goldston
Justin Nielsen and Luke Goldston, Utah State University Eastern discuss their work with Small World Initiative
Professor Wayne Hatch
Professor Wayne Hatch, Utah State University Eastern, Small World Initiative
Eli Cohen
Eli Cohen explains his research on the assembly of flagella in Salmonella
Matt Mulvey
Matt Mulvey, President of the ASM Intermountain Branch


How long does the grant writing process take?

How well do you know the grant writing process?

For a successful grant application, the typical time from submission to funding is:

a. 1-2 months
b. 3-4 months
c. 5-6 months
d. 7-8 months
e. 9-10 months

The typical length of the grant writing process, from when you begin planning your application to when you receive the funds, is 9-10 months. Since the grant process takes a significant amount of time and has important future implications, it is important to utilize all available resources. One such resource is the ASM Grant Writing Online Course. This three month, six-part webinar series provides graduate, postdoctoral sciences and early to mid-career scientists with an overview of the NIH and NSF grant process. Led by individuals who have successfully obtained grants, this course will provide participants with a broad understanding of (i) the grant making enterprise and the overall funding landscape, (ii) tips for successfully writing NIH and NSF grants, (iii) developing an impactful NIH/NSF Biosketch, and (iv) viewing your grant from the reviewer's perspective. 

Register here
Registration deadline: December 1, 2016
January - March 2017
ASM members: $150 | Non-members: $200


Hello bLogPhase reader,

I am Stefano Bertuzzi, the Chief Executive Officer of the American Society for Microbiology (ASM). I use bLogPhase to communicate my thoughts with ASM members as well as anyone interested in science and various policy issues related to science. Before joining ASM, I blogged for ASCB on similar topics.

I have a Ph.D. in Molecular Biology from the Universita' Cattolica del Sacro Cuore of Milan, Italy, and a Master's degree in Public Health from Johns Hopkins University. As a student, postdoc and PI, I was a bench researcher in the U.S. and Italy for 15 years before moving over to the science policy side at NIH in 2006. I have enjoyed every step of my scientific career and coming to the world of scientific associations has opened even wider horizons for me on what a scientist can do in modern society.

I've always liked to write. For a brief time, I had a fling considering writing as a career, and even became a registered journalist in my native Italy. But research science won out. But now, with bLogPhase I am looking at a new part time career as a blogger. As excited as I am about writing bLogPhase I realize that a blog has to be a two-way street. This blog needs your comments, corrections, additional thoughts, push back and, I hope, an occasional "Bravo." (Well, at least no rotten tomatoes.) So post your comments and your ideas. This is a space for ASM members and all those interested in the microbial sciences, science policy and science communications to interact.

Before joining ASM, I was the Executive Director of the American Society for Cell Biology (ASCB) and previously the Science Policy Director at the National Institute of Mental Health (NIMH) where I greatly enjoyed working with Tom Insel, an extraordinary scientist and advocate for research into mental disorders. Before NIMH, I was in the Office of the NIH Director, in charge of the Return on Investment Program. There, I worked with Lana Skirboll, Lynn Hudson, and Elias Zerhouni. I am indebted to all of them for infusing me with an incurable passion for public service and science policy.

My wife, Elena, and I have been together since high school. We have two young children, Davide and Celeste. I love being on the water, sailing or windsurfing. I am an avid reader as regular readers of bLogPhase will soon discover.

So follow me and please jump in with your comments.

bioRxiv (static HTML)

Genome Integration and Reactivation of the Virophage MavirusIn the Marine Protozoan Cafeteria roenbergensis


Fischer, M. G. | Hackl, T. |


Endogenous viral elements are increasingly found in eukaryotic genomes, yet little is known about their origins, dynamics, or function. Here, we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defense system. We found that the virophage mavirus, a parasite of the giant virus CroV, integrates at multiple sites within the nuclear genome of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. The endogenous mavirus is structurally and genetically similar to the eukaryotic Maverick/Polinton DNA transposons. Provirophage genes are activated by superinfection with CroV, which leads to the production of infectious mavirus particles. While provirophage-carrying cells are not directly protected from lysis by CroV, release of reactivated virophage particles promotes survival of other host populations. Our results corroborate the connection between mavirus and Maverick/Polinton elements and suggest that provirophages can defend natural protist populations against infection by giant viruses.

DOI: http://dx.doi.org/10.1101/068312

PUBLISHED: 2016-08-07

Generated MeSH Terms

Animals | DNA Transposable Elements | Parasites | Eukaryota | Superinfection | SERPINA3 protein, human | Serpins | Viruses | DNA Viruses | Antiviral Agents |

Related Articles

21385722 | 23701946 | 24973308 | 21559486 | 26305943 | 20974979 | 24747414 | 26560305 | 23071316 | 24882428

Direct correlation between motile behavior and protein abundance in single cells


Dufour, Y. S. | Gillet, S. | Frankel, N. W. | Weibel, D. B. | Emonet, T. |


Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

DOI: http://dx.doi.org/10.1101/067918

PUBLISHED: 2016-08-04

Generated MeSH Terms

Methylation | Escherichia coli | Microscopy | Polymerization | Hydrogel | Swimming | Chemotaxis | Gene Expression Regulation | 5-(2-cyclohexylidene-ethyl)-5-ethylbarbiturate | Barbiturates | Phenotype | Genetic Variation |

Related Articles

16788185 | 11717272 | 21292743 | 20972792 | 3056911 | 2188960 | 2661528 | 10464232 | 19231145 | 9465023

Rapid resistome mapping using nanopore sequencing


van der Helm, E. | Imamovic, L. | Hashim Ellabaan, M. M. | Koza, A. | Sommer, M. O. A. O. A. |


The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.

DOI: http://dx.doi.org/10.1101/067652

PUBLISHED: 2016-08-03

Generated MeSH Terms

Humans | Workflow | Nanopores | Drug Resistance, Microbial | Microbiota | Metagenomics | Bacterial Infections | Anti-Bacterial Agents | Intensive Care Units |

Related Articles

26419330 | 24710024 | 25918444 | 25247417 | 23370726 | 22827799 | 24474281 | 24236055 | 22936781 | 22954750

Experimental estimation of the effects of all amino-acid mutations to HIV Env


Haddox, H. K. | Dingens, A. S. | Bloom, J. |


HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV's most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV's growth in cell culture. We compare our experimental measurements of each site's preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. We show that some regions of Env have a high inherent tolerance to mutation, whereas other regions (such as epitopes of broadly neutralizing antibodies) have a significantly reduced capacity to tolerate mutations. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env's evolution.

DOI: http://dx.doi.org/10.1101/067470

PUBLISHED: 2016-08-02

Generated MeSH Terms

Antibodies, Neutralizing | Epitopes | Antiviral Agents | Amino Acids | Genes, env | HIV Infections | Virus Replication | Mutation |

Related Articles

18177204 | 19096508 | 24713822 | 25006036 | 17534408 | 26506369 | 8995670 | 23468626 | 10364320 | 22073263

Small molecules with antibiofilm, antivirulence and antibiotic synergy activities against Pseudomonas aeruginosa.


van Tilburg Bernardes, E. | Charron-Mazenod, L. | Reading, D. | Reckseidler-Zenteno, S. L. | Lewenza, S. |


Biofilm formation is a universal bacterial strategy for long-term survival in nature and during infections. Biofilms are dense microbial communities enmeshed within a polymeric extracellular matrix that protects bacteria from antibiotic exposure and the immune system and thus contribute to chronic infections. Pseudomonas aeruginosa is an archetypal biofilm-forming organism that utilizes a biofilm growth strategy to cause chronic lung infections in Cystic Fibrosis (CF) patients. The extracellular matrix of P. aeruginosa biofilms is comprised mainly of exopolysaccharides (EPS) and DNA. Both mucoid and non-mucoid isolates of P. aeruginosa produces the Pel and Psl EPS, each of which have important roles in antibiotic resistance, biofilm formation and immune evasion. Given the central importance of the Pel and Psl EPS in biofilm structure, they are attractive targets for novel anti-infective compounds. In this study we used a high throughput gene expression screen to identify compounds that repress expression of pel and psl genes as measured by transcriptional lux fusions. Testing of the pel/psl repressors demonstrated an antibiofilm activity against microplate and flow chamber biofilms formed by wild type and hyperbiofilm forming strains. To determine the potential role of EPS in virulence, mutants in pel/psl were shown to have reduced virulence in the feeding behavior and slow killing virulence assays in Caenorhabditis elegans. The antibiofilm molecules also reduced P. aeruginosa PAO1 virulence in the nematode slow killing model. Importantly, the combination of antibiotics and antibiofilm compounds were synergistic in killing P. aeruginosa biofilms. These small molecules represent a novel anti-infective strategy for the possible treatment of chronic P. aeruginosa infections.

DOI: http://dx.doi.org/10.1101/067074

PUBLISHED: 2016-08-01

Generated MeSH Terms

Animals | Humans | Pseudomonas aeruginosa | Biofilms | Anti-Bacterial Agents | Caenorhabditis elegans | Virulence | Cystic Fibrosis | Immune Evasion | Drug Resistance, Microbial | Anti-Infective Agents | Biological Processes | Physiological Processes | DNA | Extracellular Matrix | Immune System | Feeding Behavior |

Related Articles

21605307 | 22176658 | 24595142 | 22309106 | 21666010 | 22309122 | 25096883 | 21298031 | 21998591 | 22585230

Stochastic Assembly Produces Heterogeneous Communities in the C. elegans Intestine


Vega, N. | Gore, J. |


Host-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here we demonstrate that stochastic bacterial community assembly in the C. elegans intestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

DOI: http://dx.doi.org/10.1101/067173

PUBLISHED: 2016-08-01

Generated MeSH Terms

Animals | Caenorhabditis elegans | Stochastic Processes | Ecology | Intestines | Bacteria |

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24449749 | 23462114 | 23812817 | 21608478 | 23407312 | 24489823 | 23613815 | 22452899 | 22276219 | 26699734

Cohort Specific Effects of Cereal-bar Supplementation in Overweight Patients With or Without Type 2 Diabetes Mellitus


Lauber, C. | Chou, C. J. | Chakrabarti, A. | Siddharth, J. | Chalut-Carpentier, A. | Pataky, Z. | Golay, A. | Parkinson, S. |


The importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand diet-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-diabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g {beta}-glucan on their habitual diet for 30 days. Fecal bacterial communities in an age-matched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to cereal-bar supplementation are cohort specific and this should be considered when manipulating the microbiome via diet supplementation.

DOI: http://dx.doi.org/10.1101/066704

PUBLISHED: 2016-07-29

Generated MeSH Terms

Humans | Edible Grain | Diet, Western | RNA, Ribosomal, 16S | Diabetes Mellitus, Type 2 | Metagenomics | Microbiota | Overweight | Glucans |

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25271941 | 25954902 | 18974945 | 20368178 | 26039313 | 26147095 | 19706296 | 26066038 | 19043404 | 21121044

Capture of Vibrio cholerae by charged polymers inhibits pathogeniciy by inducing a sessile lifestyle


Perez-Soto, N. | Moule, L. | Crisan, D. N. | Insua, I. | Taylor-Smith, L. M. | Voelz, K. | Fernandez-Trillo, F. | Krachler, A. |


Vibrio cholerae, the causative agent of cholera, is an abundant environmental bacterium that can efficiently colonize the intestinal tract and trigger severe diarrheal illness. Motility, and the production of colonization factors and cholera toxin, are fundamental for the establishment of disease. In the aquatic environment, V. cholerae persists by forming avirulent biofilms on zooplankton, phytoplankton and chitin debris. Here, we describe the formation of artificial, biofilm-like communities, driven by exposure of planktonic bacteria to synthetic polymers. This recruitment is extremely rapid and charge-driven, and leads to the formation of initial 'seed clusters' which then recruit additional bacteria to extend in size. Bacteria that become entrapped in these 'forced communities' undergo transcriptional changes in motility and virulence genes, and phenotypically mimic features of environmental biofilm communities by forming a matrix that contains polysaccharide and extracellular DNA. As a result of this lifestyle transition, pathogenicity and in vivo host colonization decrease. These findings highlight the potential of synthetic polymers to disarm pathogens by modulating their lifestlye, without creating selective pressure favoring the emergence of antimicrobial resistant strains.

DOI: http://dx.doi.org/10.1101/066563

PUBLISHED: 2016-07-28

Generated MeSH Terms

Animals | Vibrio cholerae | Cholera | Cholera Toxin | Virulence | Zooplankton | Biofilms | Plankton | Phytoplankton | Chitin | Polymers | Anti-Infective Agents | Intestines | DNA | Polysaccharides | Biological Processes | Life Style |

Related Articles

25368110 | 16267135 | 19933826 | 24375135 | 22354023 | 16359328 | 14536065 | 22710417 | 22032623 | 22106284

Sequence based prediction of novel domains in the cellulosome of Ruminiclostridium thermocellum


Basharat, Z. | Yasmin, A. |


Ruminiclostridium thermocellum strain ATCC 27405 is valuable with reference to the next generation biofuel production being a degrader of crystalline cellulose. The completion of its genome sequence has revealed that this organism carries 3,376 genes with more than hundred genes encoding for enzymes involved in cellulysis. Novel protein domain discovery in the cellulose degrading enzyme complex of this strain has been attempted to understand this organism at molecular level. Streamlined automated methods were employed to generate possibly unreported or new domains. A set of 12 novel Pfam-B domains was developed after detailed analysis. This finding will enhance our understanding of this bacterium and its molecular processes involved in the degradation of cellulose. This approach of in silico analysis prior to experimentation facilitates in lab study. Previously uncorrelated data has been utilized for rapid generation of new biological information in this study.

DOI: http://dx.doi.org/10.1101/066357

PUBLISHED: 2016-07-27

Generated MeSH Terms

Cellulosomes | Biofuels | Cellulose | Clostridium thermocellum | Protein Structure, Tertiary | Multienzyme Complexes | Base Sequence |

Related Articles

12625841 | 20662379 | 21672225 | 19384422 | 21526192 | 1490597 | 21255373 | 25956772 | 20307315 | 23176123

A Novel Family of Genomics Islands Across Multiple Species of Streptococcus


Wang, J. | Wang, C. | Feng, W. | Feng, Y. | Zhi, L. | Li, W. | Yao, Y. | Jiang, S. | Tang, J. |


The genus Streptococcus is one of the most genomically diverse and important human and agricultural pathogens. The acquisition of genomic islands (GIs) plays a central role in adaptation to new hosts in the genus pathogens. The research presented here employs a comparative genomics approach to define a novel family of GIs in the genus Streptococcus which also appears across strains of the same species. Specifically, we identified 9 Streptococcus genomes out of 67 sequenced genomes analyzed, and we termed these as 15bp Streptococcus genomic islands, or 15SGIs, including i) insertion adjacent to the 3' end of ribosome l7/l12 gene, ii) large inserts of horizontally acquired DNA, and iii) the presence of mobility genes (integrase) and replication initiators. We have identified a novel family of 15SGIs and seems to be important in species differentiation and adaptation to new hosts. It plays an important role during strain evolution in the genus Streptococcus.

DOI: http://dx.doi.org/10.1101/065920

PUBLISHED: 2016-07-26

Generated MeSH Terms

Humans | Genomic Islands | Integrases | Genomics | Biological Evolution | Streptococcus | DNA | Ribosomes |

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23096693 | 17475002 | 22306813 | 21672261 | 23204461 | 18071028 | 21536150 | 24977706 | 25009843 | 20826944

Microbial Communities are Well Adapted to Disturbances in Energy Input


Fernandez-Gonzalez, N. | Huber, J. A. | Vallino, J. J. |


Although microbial systems are well-suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20 day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function was used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appear inherently well-adapted to disturbances in energy input and that changes in community structure in both treatments are more dependent on internal dynamics than on external forcing. Results also show that the rare biosphere is critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, endogenous feedbacks were more important than exogenous drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and only experience succession or replacement when subject to external perturbations, such as changes in food availability or introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.

DOI: http://dx.doi.org/10.1101/066050

PUBLISHED: 2016-07-26

Generated MeSH Terms

RNA, Ribosomal, 16S | Biota | Microbiota | Ecology |

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25028427 | 24732211 | 23462114 | 24926862 | 23985743 | 18043612 | 12755711 | 22530997 | 22286988 | 19030917

S2 from Equine infectious anemia virus is an infectivity factor which counteracts the retroviral inhibitors SERINC5 and SERINC3


Chande, A. | Cuccurullo, E. | Rosa, A. | Ziglio, S. | Carpenter, S. | Pizzato, M. |


The lentivirus equine infectious anemia virus (EIAV) encodes S2, a pathogenic determinant important for virus replication and disease progression in horses. No molecular function has yet been linked to this accessory protein. We now report that S2 can replace the activity of Nef on HIV-1 infectivity, being required to antagonize the inhibitory activity of SERINC proteins on Nef-defective HIV-1. Similar to Nef, S2 excludes SERINC5 from virus particles and requires an ExxxLL motif predicted to recruit the clathrin adaptor AP2. Accordingly, a functional endocytic machinery is essential for S2-mediated infectivity enhancement, which is impaired by inhibitors of clathrin-mediated endocytosis. In addition to retargeting SERINC5 to a late endosomal compartment, S2 promotes the host factor degradation. Emphasizing the similarity with Nef, we show that S2 is myristoylated and, compatible with a crucial role of the post-translational modification, its N-terminal glycine is required for the anti-SERINC5 activity. EIAV-derived vectors devoid of S2 are less susceptible than HIV-1 to the inhibitory effect of both human and equine SERINC5. We then identified the envelope glycoprotein of EIAV as a determinant which also modulates retrovirus susceptibility to SERINC5, indicating a bi-modular ability of the equine lentivirus to counteract the host factor. S2 shares no sequence homology with other retroviral factors known to counteract SERINC5. Adding to primate lentivirus Nef and gammaretrovirus glycoGag, the accessory protein from EIAV makes another example of a retroviral virulence determinant which independently evolved SERINC5-antagonizing activity. SERINC5 therefore plays a critical role for the interaction of the host with diverse retrovirus pathogens.

DOI: http://dx.doi.org/10.1101/065078

PUBLISHED: 2016-07-21

Generated MeSH Terms

Humans | Horses | Animals | Infectious Anemia Virus, Equine | HIV-1 | Lentiviruses, Primate | Virion | Lentivirus | Gammaretrovirus | Retroviridae | Lentiviruses, Equine | Protein Processing, Post-Translational | Glycine | Virulence | Equidae | Virus Replication | HIV Infections | Sequence Homology | Endocytosis | Disease Progression | Clathrin | Adaptor Proteins, Vesicular Transport |

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26416734 | 26416733 | 10590152 | 20417672 | 17267500 | 16503341 | 15539516 | 19769166 | 25390683 | 18057237

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology


Hall, E. | Bernhardt, E. | Bier, R. | Bradford, M. | Boot, C. | Cotner, J. | del Giorgio, P. | Evans, S. | Graham, E. | Jones, S. | Lennon, J. | Locey, K. | Nemergut, D. | Osborne, B. | Rocca, J. | Schimel, J. | Waldrop, M. | Wallenstein, M. |


The well-documented significance of microorganisms to the function of virtually all ecosystems has led to the assumption that more information on microbiomes will improve our ability to understand and predict system-level processes. Notably, the importance of the microbiome has become increasingly evident in the environmental sciences and in particular ecosystem ecology. However, translating the ever-increasing wealth of information on environmental microbiomes to advance ecosystem science is proving exceptionally challenging. One reason for this challenge is that correlations between microbiomes and the ecosystem processes they influence are often reported without the underlying causal mechanisms. This limits the predictive power of each correlation to the time and place at which it was identified. In this paper, we assess the assumptions and approaches currently used to establish links between environmental microbiomes and the ecosystems they influence, propose a framework to more effectively harness our understanding of microbiomes to advance ecosystem science, and identify key challenges and solutions required to apply the proposed framework. Specifically, we suggest identifying each microbial process that contributes to the ecosystem process of interest a priori. We then suggest linking information on microbial community membership through microbial community properties (such as biomass elemental ratios) to the microbial processes that drive each ecosystem process (e.g. N -mineralization). A key challenge in this framework will be identifying which microbial community properties can be determined from the constituents of the community (community aggregated traits, CATs) and which properties are unable to be predicted from a list of their constituent taxa (emergent properties, EPs). We view this directed approach as a promising pathway to advance our understanding of how microbiomes influence the systems they inhabit.

DOI: http://dx.doi.org/10.1101/065128

PUBLISHED: 2016-07-21

Generated MeSH Terms

Biomass | Ecology | Microbiota |

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26200800 | 26422463 | 26378320 | 20662931 | 26380076 | 18695234 | 23462114 | 21272182 | 26207269 | 25880923

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition


Knudsen, B. E. | Bergmark, L. | Munk, P. | Lukjancenko, O. | Prieme, A. | Aarestrup, F. M. | Pamp, S. J. |


Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare a total of eight DNA extraction procedures for three specimen types (human feces, pig feces, hospital sewage), assess DNA extraction using spike-in controls and different types of beads for bead-beating facilitating cell lysis. We evaluate DNA concentration, purity, and stability, and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead-beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate compared to standard protocols. Based on this insight, we have designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens.

DOI: http://dx.doi.org/10.1101/064394

PUBLISHED: 2016-07-18

Generated MeSH Terms

Humans | Animals | Swine | Sewage | RNA, Ribosomal, 16S | Anti-Infective Agents | Metagenomics | Microbiota | DNA | Genomics | Feces | Bacteria |

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26094313 | 22457796 | 23844068 | 25880246 | 20140796 | 25548939 | 25257543 | 25798612 | 24884524 | 25549184



Khambhala, P. | Paliwal, P. | Kothari, V. |


Microwave mutagenesis of Brevibacillus parabrevis for enhanced cellulase production was attempted. Though microwave treatment could alter the cellulase activity of the test bacterium, none of the mutants obtained were found to be genetically stable, indicating the reversible nature of microwave-induced mutation(s). Thermal stability of the B. parabrevis cellulase was also investigated. This enzyme was found to be capable of retaining its activity even after heat treatment (50-121{degrees}C, for 30-60 min). Fluorescence spectrum revealed a red shift in the emission maxima of the heat-treated enzyme preparations, indicating some structural change upon heating, but no major loss of activity was observed. This enzyme was found to be active over a broad temp range, with 90{degrees}C as the optimum temp, which is interesting as the producing organism is a mesophile.

DOI: http://dx.doi.org/10.1101/064410

PUBLISHED: 2016-07-18

Generated MeSH Terms

Cellulase | Heating | Microwaves | Brevibacillus | Fluorescence | Hot Temperature | Temperature | Hyperthermia, Induced | Mutagenesis | Mutation |

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19656667 | 12153 | 19859753 | 25886936 | 11272024 | 780122 | 11854 | 19711200 | 11341679 | 15659186

Comparative phylogenetic analysis of bacterial associates in Pyrrhocoroidea and evidence for ancient and persistent environmental symbiont reacquisition in Largidae (Hemiptera: Heteroptera).


Gordon, E. R. L. | McFrederick, Q. S. | Weirauch, C. |


The ancient insect order Hemiptera, one of the most well-studied insect lineages with respect to bacterial symbioses, still contains major branches which lack robust phylogenies and comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species]; Pyrrhocoridae [~300 species]) is a superfamily of the primarily-herbivorous hemipteran infraorder Pentatomomorpha, though relationships to related superfamilies are controversial. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes between these putative sister families. We surveyed bacterial diversity of this group using paired-end Illumina and targeted Sanger sequencing of bacterial 16S amplicons of 30 pyrrhocoroid taxa, including 17 species of Largidae, in order to determine the identity of bacterial associates and similarity of associated microbial communities among species. We also constructed the first comprehensive phylogeny of this superfamily (4,800 bp; 5 loci; 57 ingroup + 12 outgroup taxa) in order accurately trace the evolution of symbiotic complexes among Pentatomomorpha. We undertook multiple lines of investigation (i.e., experimental rearing, FISH microscopy, phylogenetic and co-evolutionary analyses) to understand potential transmission routes of largid symbionts. We found a prevalent, specific association of Largidae with plant-beneficial-environmental clade Burkholderia housed in midgut tubules. As in other distantly-related Heteroptera, symbiotic bacteria seem to be acquired from the environment every generation. We review current understanding of symbiotic complexes within the Pentatomomorpha and discuss means to further investigations of the evolution and function of these symbioses. Importance. Obligate symbioses with bacteria are common in insects, particularly for Hemiptera wherein varied forms of symbiosis occur, though knowledge of symbionts remains incomplete for major lineages. Thus, an accurate understanding of how these partnerships evolved and changed over millions of years is not yet achievable. We contribute to our understanding of the evolution of symbiotic complexes in Hemiptera by characterizing bacterial associates of Pyrrhocoroidea focusing on the family Largidae and by constructing a phylogeny to establish evolutionary relationships of and within this group. Members of Largidae are associated with specific symbiotic Burkholderia from a different clade than Burkholderia symbionts in other Hemiptera and are members of the earliest-diverging superfamily of Burkholderia-associated Hemiptera. Evidence suggests that species of Largidae reacquire specific symbiotic bacteria every generation environmentally, a rare strategy for insects with potentially volatile evolutionary ramifications, but one that has persisted in Largidae and other related lineages since the Cretaceous.

DOI: http://dx.doi.org/10.1101/064022

PUBLISHED: 2016-07-15

Generated MeSH Terms

Animals | Female | Heteroptera | Phylogeny | Symbiosis | Burkholderia | Siblings | Microscopy | Biological Evolution | Herbivory | Residence Characteristics |

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26023876 | 25521625 | 19146674 | 20882057 | 23574391 | 26116716 | 21385056 | 23949857 | 23691052 | 26045536

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei With Increased Virulence or Fluoroquinolone Resistance


Kozyreva, V. K. | Jospin, G. | Greninger, A. | Watt, J. P. | Eisen, J. A. | Chaturvedi, V. |


Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 - 2015. Preliminary data indicated the involvement of two distinct yet related bacterial populations, one from San Diego and San Joaquin (SD/SJ) and one from the San Francisco (SF) Bay area. Whole genome sequencing of sixty-eight outbreak and archival isolates of S. sonnei was performed to investigate the microbiological factors related to these outbreaks. Both SD/SJ and SF populations, as well as almost all of the archival S. sonnei isolates belonged to sequence type 152 (ST152). Genome-wide SNP analysis clustered the majority of California (CA) isolates to an earlier described global Lineage III, which has persisted in CA since 1986. Isolates in the SD/SJ population had a novel Shiga-toxin (STX)-encoding lambdoid bacteriophage, most closely related to that found in an Escherichia coli O104:H4 strain responsible for a large outbreak. However, the STX genes (stx1a and stx1b) from this novel phage had sequences most similar to the phages from S. flexneri and S. dysenteriae. The isolates in the SF population yielded evidence of fluoroquinolone resistance acquired via the accumulation of point mutations in gyrA and parC genes. Thus, the CA S. sonnei lineage continues to evolve by the acquisition of increased virulence and antibiotic resistance, and enhanced monitoring is advocated for its early detection in future outbreaks.

DOI: http://dx.doi.org/10.1101/063818

PUBLISHED: 2016-07-14

Generated MeSH Terms

Shigella sonnei | Dysentery, Bacillary | Shiga Toxin | Virulence | San Francisco | Point Mutation | Escherichia coli | Bays | Drug Resistance, Microbial | Fluoroquinolones | Bacteriophages | Disease Outbreaks |

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11705937 | 23390901 | 22858547 | 19297378 | 23341549 | 11699845 | 9623912 | 3049838 | 17587439 | 20947666

Microbial Mat Functional and Compositional Sensitivity to Environmental Disturbance


Preisner, E. C. | Fichot, E. B. | Norman, R. S. |


The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the activity of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. While this ecosystem undergoes a range of seasonal variation, it experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and activity of abundant and rare taxa, suggesting overall functional and compositional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low activity across conditions, the total number of active taxa and overall activity increased post-disturbance, with significant shifts in activity occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and activity. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.

DOI: http://dx.doi.org/10.1101/063370

PUBLISHED: 2016-07-12

Generated MeSH Terms

Archaea | Nitrification | Nitrogen | RNA, Ribosomal, 16S | Crenarchaeota | Denitrification | Sulfur | Seasons | Euryarchaeota | Salinity | Proteobacteria | Halobacterium | Cyclonic Storms | Bahamas | Genes, rRNA | Biodiversity | Ecosystem | Cyanobacteria | Islands | Polymerase Chain Reaction | Sulfates |

Related Articles

25028427 | 25781013 | 24704080 | 26474747 | 17298358 | 23254515 | 25912922 | 22194288 | 25423027 | 26283343

Benzoate and Salicylate Tolerant Strains Lose Antibiotic Resistance during Laboratory Evolution of Escherichia coli K-12


Creamer, K. | Ditmars, F. | Basting, P. J. | Acero, S. | Kunka, K. S. | Hamdallah, I. | Bush, S. P. | Scott, Z. | He, A. | Penix, S. | Gonzales, A. | Eder, E. K. | Camperchioli, D. | Berndt, A. | Clark, M. W. | Rouhier, K. | Slonczewski, J. L. |


Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted laboratory evolution by daily dilution in increasing concentrations of benzoic acid (from 5 to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from the evolving populations showed change in phenotype from benzoate-sensitive to benzoate-tolerant but sensitive to chloramphenicol and tetracycline. Sixteen clones isolated at 2,000 generations grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth profiles were seen in 10 mM salicylate. The strains showed growth profiles indistinguishable from W3110 in the absence of benzoate; in media buffered at pH 4.8, pH 7.0, or pH 9.0; or in 20 mM acetate or sorbate at pH 6.5. The genomes of 16 strains revealed over 100 mutations including SNPs, large deletions, and insertion sequence knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or associated regulators such as rob and cpx, as well as MDR efflux pumps emrA, emrY, and mdtA. Strains also lost or down-regulated the Gad acid fitness regulon. In 5 mM benzoate, or in 2 mM salicylate, most strains showed increased sensitivity to the antibiotic chloramphenicol, some more sensitive than a marA knockout. Thus, the benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance.

DOI: http://dx.doi.org/10.1101/063271

PUBLISHED: 2016-07-11

Generated MeSH Terms

Tetracycline | Chloramphenicol | Benzoic Acid | Food Preservatives | DNA Transposable Elements | Aspirin | Escherichia coli | Benzoates | Escherichia coli K12 | Regulon | Down-Regulation | Gastrointestinal Microbiome | Polymorphism, Single Nucleotide | Drug Resistance, Microbial | Salicylates | Anti-Bacterial Agents | Acids | Phenotype | Drug Resistance, Multiple | Mutation | Acetates |

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25556191 | 7504664 | 3909154 | 20011599 | 15496390 | 2954947 | 21541325 | 9097440 | 1537798 | 11257026

Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain


Ambros, S. | Martinez, F. | Ivars, P. | Hernandez, C. | de la Iglesia, F. | Elena, S. F. |


Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Koch's postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

DOI: http://dx.doi.org/10.1101/063255

PUBLISHED: 2016-07-11

Generated MeSH Terms

Tobamovirus | Lycopersicon esculentum | Host Specificity | RNA | Spain | Base Sequence | Plant Viruses | Sequence Homology | Piper nigrum | Molecular Diagnostic Techniques | RNA Viruses |

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14579173 | 22080188 | 21853328 | 24390328 | 19768650 | 26239043 | 19423673 | 20470828 | 22523958 | 23064695

An ex vivo lung model to study bronchioles infected with Pseudomonas aeruginosa biofilms


Harrison, F. | Diggle, S. P. |


A key aim in microbiology is to determine the genetic and phenotypic bases of bacterial virulence, persistence and antimicrobial resistance in chronic biofilm infections. This requires tractable, high-throughput models that reflect the physical and chemical environment encountered in specific infection contexts. Such models will increase the predictive power of microbiological experiments and provide platforms for enhanced testing of novel antibacterial or antivirulence therapies. We present an optimised ex vivo model of cystic fibrosis lung infection: ex vivo culture of pig bronchiolar tissue in artificial cystic fibrosis mucus. We focus on the formation of biofilms by Pseudomonas aeruginosa. We show highly repeatable and specific formation of biofilms that resemble clinical biofilms by a commonly-studied lab strain and ten cystic fibrosis isolates of this key opportunistic pathogen.

DOI: http://dx.doi.org/10.1101/063222

PUBLISHED: 2016-07-11

Generated MeSH Terms

Animals | Swine | Pseudomonas aeruginosa | Cystic Fibrosis | Biofilms | Anti-Bacterial Agents | Bronchioles | Virulence | Anti-Infective Agents | Mucus | Pseudomonas Infections | Lung | Sus scrofa |

Related Articles

26506004 | 16207991 | 21998591 | 17116883 | 25448466 | 11048725 | 22309106 | 26253522 | 17224667 | 25477303

Origins of pandemic clones from environmental gene pools


Shapiro, B. J. | Levade, I. | Kovacikova, G. | Taylor, R. K. | Almagro-Moreno, S. |


Some microbes can transition from an environmental lifestyle to a pathogenic one. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes. However, the genomic features that must be present in a population prior to the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, using Vibrio cholerae as a model. We then characterized several environmental VAP alleles to show that one of them reduced the ability of clinical strains to colonize a mammalian host, whereas two other alleles conferred efficient colonization. These results show that VAPs are present in environmental bacterial populations prior to the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment, they become selected and enriched under certain ecological conditions, and finally a genomic background containing several VAPs acquires virulence factors that allows for its emergence as a pathogenic clone.

DOI: http://dx.doi.org/10.1101/063115

PUBLISHED: 2016-07-10

Generated MeSH Terms

Animals | Vibrio cholerae | Virulence | Alleles | Virulence Factors | Gene Pool | Pandemics | Ecology | Genomics | Mammals | Life Style |

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14766976 | 18462070 | 23076327 | 19319196 | 11939579 | 22676367 | 14607067 | 15728357 | 10024551 | 21078967

Metabolic Reconstruction and Modeling Microbial Electrosynthesis


Marshall, C. | Ross, D. | Handley, K. | Weisenhorn, P. | Edirisinghe, J. | Henry, C. | Gilbert, J. | May, H. | Norman, R. S. |


Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial taxa to capture electrons from a cathode and fix carbon. Yet the metabolic capacity of multispecies microbial communities on electrosynthetic biocathodes remains unknown. We assembled 13 genomes from a high-performing electroacetogenic culture, and mapped their transcriptional activity from a range of conditions. This allowed us to create a metabolic model of the primary community members (Acetobacterium, Sulfurospirillum, and Desulfovibrio). Acetobacterium was the primary carbon fixer, and a keystone member of the community. Based on transcripts upregulated near the electrode surface, soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were essential conduits for electron flow from the electrode into the electrosynthetic community. A nitrogenase gene cluster with an adjacent ferredoxin and one of two Rnf complexes within the genome of the Acetobacterium were also upregulated on the electrode. Nitrogenase is known to serve as a hydrogenase, thereby it would contribute to hydrogen production by the biocathode. Oxygenases of microaerobic members of the community throughout the cathode chamber, including Sulfurospirillum and Rhodobacteraceae, were expressed. While the reactors were maintained anaerobically, this gene expression would support anaerobic growth and thus electrosynthesis by scrubbing small amounts of O2 out of the reactor. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.

DOI: http://dx.doi.org/10.1101/059410

PUBLISHED: 2016-07-07

Generated MeSH Terms

Acetobacterium | Hydrogenase | Ferredoxins | Formate Dehydrogenases | Desulfovibrio | Electrons | Rhodobacteraceae | Nitrogenase | Carbon | Oxygenases | Electrodes | Renewable Energy | Biological Processes | Up-Regulation | Multigene Family | Hydrogen | Cytochromes |

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23676111 | 23001672 | 26399888 | 26079858 | 24910339 | 17353934 | 18284174 | 23603672 | 24126154 | 25333313

Characterization of the effects of n-butanol on the cell envelope of E. coli


Fletcher, E. | Pilizota, T. | Davies, P. R. | McVey, A. | French, C. E. |


Biofuel alcohols have severe consequences on the microbial hosts used in their biosynthesis, which limits the productivity of the bioconversion. The cell envelope is one of the most strongly affected structures, in particular, as the external concentration of biofuels rises during biosynthesis. Damage to the cell envelope can have severe consequences, such as impairment of transport into and out of the cell; however the nature of butanol-induced envelope damage has not been well characterized. In the present study, the effects of n-butanol on the cell envelope of Escherichia coli were investigated. Using enzyme and fluorescence-based assays, we observed that 1% v/v n-butanol resulted in release of lipopolysaccharides from the outer membrane of E. coli and caused leakiness in both outer and inner membranes. Higher concentrations of n-butanol, within the range of 2% - 10% (v/v), resulted in inner membrane protrusion through the peptidoglycan observed by characteristic blebs. The findings suggest that strategies for rational engineering of butanol-tolerant bacterial strains should take into account all components of the cell envelope.

DOI: http://dx.doi.org/10.1101/062547

PUBLISHED: 2016-07-07

Generated MeSH Terms

1-Butanol | Peptidoglycan | Escherichia coli | Lipopolysaccharides | Biofuels | Alcohols | Fluorescence | Blister | Butanols | Cell Membrane | Cell Wall | Biological Transport |

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24056459 | 21408113 | 20118358 | 6630230 | 22898718 | 2045784 | 24014527 | 6415062 | 24967819 | 17506684

The clinically approved antiviral drug sofosbuvir impairs Brazilian zika virus replication


Sacramento, C. Q. | de Melo, G. R. | Rocha, N. | Hoelz, L. V. B. | Mesquita, M. | de Freitas, C. S. | Fintelman-Rodrigues, N. | Marttorelli, A. | Ferreira, A. C. | Barbosa-Lima, G. | Bastos, M. M. | Volotao, E. d. M. | Tschoeke, D. A. | Leomil, L. | Bozza, F. A. | Bozza, P. T. | Boechat, N. | Thompson, F. L. | de Filippis, A. M. B. | Bruning, K. | Souza, T. |


Zika virus (ZIKV) is a member of Flaviviridae family, as other agents of clinical significance, such as dengue (DENV) and hepatitis C (HCV) viruses. ZIKV spread from Africa to Pacific and South American territories, emerging as an etiological pathogen of neurological disorders, during fetal development and in adulthood. Therefore, antiviral drugs able to inhibit ZIKV replication are necessary. Broad spectrum antivirals, such as interferon, ribavirin and favipiravir, are harmful for pregnant animal models and women. The clinically approved uridine nucleotide analog anti-HCV drug, sofosbuvir, has not been affiliated to teratogenicity. Sofosbuvir target the most conserved protein over the members of the Flaviviridae family, the viral RNA polymerase. We thus studied ZIKV susceptibility to sofosbovir. We initially characterized a Brazilian ZIKV strain for use in experimental assays. Sofosbuvir inhibits the Brazilian ZIKV replication in a dose-dependent manner, both in BHK-21 cells and SH-Sy5y, by targeting ZIKV RNA polymerase activity, with the involvement of conserved amino acid residues over the members of Flaviviridae family. The identification of clinically approved antiviral drugs endowed with anti-ZIKV could reduce the time frame in pre-clinical development. Altogether, our data indicates that sofosbuvir chemical structure is endowed with anti-ZIKV activity.

DOI: http://dx.doi.org/10.1101/061671

PUBLISHED: 2016-07-06

Generated MeSH Terms

Humans | Animals | Female | Antiviral Agents | Ribavirin | Interferons | Sofosbuvir | RNA, Viral | favipiravir | Uridine | Zika Virus | Hepatitis C Antibodies | Hepacivirus | Hepatitis C | Amides | Pyrazines | DNA-Directed RNA Polymerases | Dengue | Amino Acids | Virus Replication | Models, Animal | Fetal Development | Nervous System Diseases | Africa | Brazil |

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26085147 | 26283013 | 26294237 | 19788800 | 26527535 | 25822283 | 24148652 | 22389730 | 22953014 | 25175944

General calibration of microbial growth in microplate readers


Stevenson, K. | McVey, A. F. | Clark, I. B. N. | Swain, P. S. | Pilizota, T. |


Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from antibiotic efficacy studies, studies of growth under different nutritional or stress environments, to studies of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.

DOI: http://dx.doi.org/10.1101/061861

PUBLISHED: 2016-07-04

Generated MeSH Terms

Calibration | Biological Processes | Physiological Processes | Cell Count | Research | Anti-Bacterial Agents |

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17061075 | 22280888 | 16313423 | 24654390 | 4005611 | 10624324 | 19726895 | 21509987 | 23016461 | 22947163

Dysregulation of Long Non-coding RNA (lncRNA) Genes and Predicted lncRNA-protein Interactions during Zika Virus Infection


Ramaiah, A. | Contreras, D. | Gangalapudi, V. | Padhye, M. S. | Tang, J. | Arumugaswami, V. |


Zika Virus (ZIKV) is a causative agent for poor pregnancy outcome and fetal developmental abnormalities, including microcephaly and eye defects. As a result, ZIKV is now a confirmed teratogen. Understanding host-pathogen interactions, specifically cellular perturbations caused by ZIKV, can provide novel therapeutic targets. In order to complete viral replication, viral pathogens control the host cellular machineries and regulate various factors, including long non-coding RNA (lncRNA) genes, at transcriptional levels. The role of lncRNA genes in the pathogenesis of ZIKV-mediated microcephaly and eye defects is currently unknown. To gain additional insights, we focused on profiling the differentially expressed lncRNA genes during ZIKV infection in mammalian cells. For this study, we employed a contemporary clinical Zika viral isolate, PRVABC59, of Asian genotype. We utilized an unbiased RNA sequencing approach to profile the lncRNA transcriptome in ZIKV infected Vero cells. We identified a total of 121 lncRNA genes that are differentially regulated at 48 hours post-infection. The majority of these genes are independently validated by reverse-transcription qPCR. A notable observation was that the lncRNAs, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and NEAT1 (Nuclear Paraspeckle Assembly Transcript 1), are down-regulated upon Zika viral infection. MALAT1 and NEAT1 are known as nuclear localized RNAs that regulate gene expression and cell proliferation. Protein-lncRNA interaction maps revealed that MALAT1 and NEAT1 share common interacting partners and form a larger network comprising of 71 cellular factors. ZIKV-mediated dysregulation of these two regulatory lncRNAs can alter the expression of respective target genes and associated biological functions, an important one being cell division. In conclusion, this investigation is the first to provide insight into the biological connection of lncRNAs and ZIKV which can be further explored for developing antiviral therapy and understanding fetal developmental processes.

DOI: http://dx.doi.org/10.1101/061788

PUBLISHED: 2016-07-01

Generated MeSH Terms

Humans | Animals | Cercopithecus aethiops | Female | Pregnancy | RNA, Long Noncoding | Adenocarcinoma of lung | Vero Cells | Teratogens | Transcriptome | Sequence Analysis, RNA | RNA, Nuclear | Host-Pathogen Interactions | Microcephaly | Pregnancy Outcome | Zika Virus | Zika Virus Infection | Adenocarcinoma | Lung Neoplasms | Virus Replication | Cell Division | Antiviral Agents | Genotype |

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When is a bacterial "virulence factor" really virulent?


Granato, E. T. | Harrison, F. | Kummerli, R. | Ross-Gillespie, A. |


Bacterial traits that contribute to disease are termed 'virulence factors' and there is much interest in therapeutic approaches that disrupt such traits. However, ecological theory predicts disease severity to be multifactorial and context dependent, which might complicate our efforts to identify the most generally important virulence factors. Here, we use meta-analysis to quantify disease outcomes associated with one well-studied virulence factor - pyoverdine, an iron-scavenging compound secreted by the opportunistic pathogen Pseudomonas aeruginosa. Consistent with ecological theory, we found that the effect of pyoverdine, albeit frequently contributing to disease, varied considerably across infection models. In many cases its effect was relatively minor, suggesting that pyoverdine is rarely essential for infections. Our work demonstrates the utility of meta-analysis as a tool to quantify variation and overall effects of purported virulence factors across different infection models. This standardised approach will help us to evaluate promising targets for anti-virulence approaches.

DOI: http://dx.doi.org/10.1101/061317

PUBLISHED: 2016-06-29

Generated MeSH Terms

Pseudomonas aeruginosa | Virulence | Virulence Factors | pyoverdin | Iron | Oligopeptides | Iron Compounds | Ecology | Reference Standards |

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Characterization of Methicillin-resistant Staphylococcus aureus Isolates from Fitness Centers in Memphis Metropolitan Area, USA


Mukherjee, N. | Sulaiman, I. M. | Banerjee, P. |


Indoor skin-contact surfaces of public fitness centers may serve as reservoirs of potential human transmission of methicillin-resistant Staphylococcus aureus (MRSA). We found a high prevalence of multi-drug resistant (MDR)-MRSA of CC59 lineage harboring a variety of extracellular toxin genes from surface swab samples collected from inanimate surfaces of fitness centers in Memphis metropolitan area, USA. Our findings underscore the role of inanimate surfaces as potential sources of transmission of MDR-MRSA strains with considerable genetic diversity.

DOI: http://dx.doi.org/10.1101/061044

PUBLISHED: 2016-06-29

Generated MeSH Terms

Humans | Methicillin-Resistant Staphylococcus aureus | Methicillin | Fitness Centers | Prevalence | Staphylococcal Infections | Staphylococcus aureus | Genetic Variation | Toxins, Biological |

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25479039 | 11144421 | 25789579 | 25200331 | 26035662 | 26063853 | 18675154 | 24039803 | 26408138 | 26113228

Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors.


Emmott, E. | Sorgeloos, F. | Caddy, S. L. | Vashist, S. | Sosnovtsev, S. | Lloyd, R. | Heesom, K. | Goodfellow, I. |


Noroviruses produce viral RNAs lacking a 5' cap structure and instead use a virus-encoded VPg protein covalently linked to viral RNA to interact with translation initiation factors and drive viral protein synthesis. Norovirus infection results in the induction of the innate response leading to interferon stimulated gene (ISG) transcription. However the translation of the induced ISG mRNAs is suppressed. Using a novel mass spectrometry approach we demonstrate that diminished host mRNA translation correlates with changes to the composition of the eukaryotic initiation factor complex. The suppression of host ISG translation correlates with the activity of the viral protease (NS6) and the activation of cellular caspases leading to the establishment of an apoptotic environment. These results indicate that noroviruses exploit the differences between viral VPg-dependent and cellular cap-dependent translation in order to diminish the host response to infection.

DOI: http://dx.doi.org/10.1101/060772

PUBLISHED: 2016-06-26

Generated MeSH Terms

RNA, Viral | Norovirus | RNA, Messenger | Interferons | Interferon Inducers | Caspases | Eukaryotic Initiation Factors | Viral Proteins | Peptide Initiation Factors | Mass Spectrometry |

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Vincent Racaniello 300

Hello everyone,

I am Vincent Racaniello, Higgins Professor of Microbiology & Immunology at Columbia University College of Physicians and Surgeons. I am using Zika Diaries to communicate the experiences of my laboratory as it moves from working on poliovirus (for 35 years) to Zika virus.

I was fortunate to be trained in virology by two brilliant virologists. I obtained my Ph.D. with Peter Palese at Mt. Sinai School of Medicine in New York City. As his first student, I received a great deal of attention as I worked on influenza viruses. For my postdoctoral work I was lucky to work with David Baltimore, just a few years after he received his Nobel Prize. In his laboratory at MIT I produced the first infectious DNA copy of an animal virus, a finding that revolutionized the study of viruses. I moved to Columbia in 1982 to start my own laboratory. Over the years our main focus has been on poliovirus.

Halfway into my research career, I developed an interest in science communication. I became part of the team that produced the ASM textbook 'Principles of Virology' in 2000. Having learned about all viruses (not just poliovirus), I wanted to share this knowledge with the public. Blogging had just become much easier, so in 2004 I started writing at virology blog (virology.ws), which I continue to this day. I also produce, with ASM, a suite of science podcasts, including the flagship This Week in Virology (microbe.tv). When I decided to teach an undergraduate virology course at Columbia University, I recorded all my lectures and released them at YouTube. All of these efforts are enhanced by the ability to reach millions via Twitter, Facebook, and other internet based technologies. You know where to find me - just google me.

Despite all this fun and fascinating activity, I jumped at the opportunity to write a new blog for ASM. Zika virus moved into world view in 2015 and many virologists, including myself, have moved to work on this important virus. I thought it would be illuminating to provide a weekly, personal view of our success and failures. All centered on an image from my laboratory (yes, I’m also at Instagram.com/profvrr).

Questions and comments are always welcome.

Agar Art Calendar


ASM Agar Art Calendar (July 2016 - June 2017)

Featuring the winners of the 2015 Agar Art Contest, along with People's Choice winners, the Agar Art Calendar is a first of its kind!
Available for $18 (includes domestic shipping), this calendar is a must have for any microbiology fan!

Sample Images:
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ASM Membership: Perceptions Needs and Challenges


Key Findings of the Membership Survey Report

students at poster


This report summarizes the key findings of an online survey conducted by Cell Associates on behalf of the American Society for Microbiology (ASM). The membership group at ASM was interested in learning more about the needs and perceptions of its members with regard to membership in the society to aid in developing a strategic plan.

To accomplish this, an online survey was conducted from November 19 through November 23, 2015. During the period that the survey was open, a total of 1,020 qualified surveys were submitted. The responses from these individuals serve as the basis for this report.

Demographics of Survey Respondents

Location: Seventy-one percent (71%) of the survey respondents were located in North America, 13% were in Europe, 8% were in Asia, and the remaining 8% were in other parts of the world.

Affiliations: Two-thirds (69%) of the survey respondents were affiliated with universities/academe. Nine percent (9%) worked in government organizations. Five percent (5%) worked in hospital/medical settings while an equal percentage worked in biotech/pharma/CROs.

Work or Study: The top three areas of work or study were molecular biology and physiology (34%), host-microbe biology (32%), and applied and environmental science (27%). Other areas were cited somewhat less often: teaching and education (21%), clinical science and epidemiology (16%), therapeutics and prevention (12%), and ecological and evolutionary science (10%).

Age: Twenty-five percent (25%) of the survey respondents were less than 35 years of age. Twenty-eight percent (28%) were 35 to 49 years old. Thirty-five percent (35%) were 50 to 64 years old. Eleven percent (11%) were 65 years or older.

Work Status: Seventeen percent (17%) of the survey respondents were students, 78% were in some phase of their working career, and 5% were retired.

Gender: 52% were male, 47% were female, and 1% preferred not to respond.

Key Findings of the Survey

Factors in Joining a Professional Society or Association

The factor that most influenced the decision to join a professional society or association was access to relevant, up-to-date information, which was cited by 65% of the survey respondents. Other factors that were cited less often include networking (42%), discounts for meetings and courses (40%), peers and colleagues being members (32%), and cost (29%).

2or3reasonsASM Membership

Approximately one-third (35%) of the survey respondents were ASM members for 3 years or less. One-fifth (22%) were members for 4 to 9 years. Thirty-seven percent (37%) of the respondents were members for 10 or more years.

The most common ways that survey respondents first learned about ASM were from faculty (37%), from colleagues (25%), and from publications (15%).

The most common reasons for becoming an ASM member were for professional or career development (54%), to learn about the latest advances in one’s field (51%), to access ASM journals (45%), and to present one’s research (42%).

A majority (72%) of the survey respondents belonged to other professional societies or organizations. Twenty-six percent (26%) of the respondents only belonged to ASM.

Awareness/Recognition of ASM Benefits

When asked which benefits ASM provides, the top responses were “opportunities to publish/present my research” (67%), “advocacy for the microbial sciences” (62%), and “a place for the microbial sciences to thrive” (61%). “Educational opportunities” (56%), “networking opportunities” (53%), “access to experts in my field” (41%), and “access to potential research collaborators” (34%) were cited somewhat less often.

Importance of ASM Member Benefits

The most important ASM member benefits were journals (61%) and Microbe magazine (48%). Other benefits were cited less often: discounts to meetings (36%), general and/or ICAAC meeting (31%), networking opportunities (31%), books and manuals (29%), ASM website (29%), and career and professional development programs (25%).

Recommending ASM to Colleagues

The vast majority (91%) of survey respondents recommended ASM membership to their colleagues to one degree or another.

Current Member Challenges

The professional challenges that members currently faced most often were funding (55%) and keeping current in one’s field (52%). Maintaining a competitive research program (34%), limited resources apart from funding (27%), networking (26%), and learning about career opportunities (24%) were cited less often.

ASM’s Focus on Members’ Fields of Interestprofessional challenges

A majority (73%) of the survey respondents felt that ASM provides sufficient focus on their field of work or study. Ten percent (10%) of the respondents felt that ASM does not provide sufficient focus on their fields. The remaining 17% were not sure.

Areas That Members Would Like to See ASM Provide More Focus On

Regarding what survey respondents would like to see more of from ASM in the future, the top two response categories were more focus on their disciplines (19%) and various items concerning meetings (16%). Other types of responses cited less often included careers (11%), networking (11%), grants, funding (10%), professional development (8%), communications (7%), and publications (7%).

What One Thing Respondents Would Most Like to See ASM Provide for Members

Survey respondents were asked what one thing they would like to see ASM provide for members at their career stage. Respondents most wanted to see more focus on grants, funding (21%), networking (15%), and careers (12%). Several other types of responses were cited less often, including professional development (9%), job listings (8%), seniors/retirement planning (6%), and communications (6%).






FACT SHEET: Preparing for and Responding to the Zika Virus at Home and Abroad


Office of the Press Secretary


February 8, 2016


FACT SHEET:  Preparing for and Responding to the Zika Virus at Home and Abroad

Since late last year, the Administration has been aggressively working to combat Zika, a virus primarily spread by mosquitoes that has recently been linked to birth defects and other concerning health outcomes.  The Federal Government has been monitoring the Zika virus and working with our domestic and international public health partners to alert healthcare providers and the public about Zika; provide public health laboratories with diagnostic tests; and detect and report cases both domestically and internationally. 

The Administration is taking every appropriate measure to protect the American people, and today announced that it is asking Congress for more than $1.8 billion in emergency funding to enhance our ongoing efforts to prepare for and respond to the Zika virus, both domestically and internationally.  The Administration will submit a formal request to Congress shortly.

The Pan American Health Organization reports 26 countries and territories in the Americas with local Zika transmission.  While we have not yet seen transmission of the Zika virus by mosquitoes within the continental United States, Puerto Rico and other U.S. territories in warmer areas with Aedes aegpyti mosquito populations are already seeing active transmission. In addition, some Americans have returned to the continental U.S. from affected countries in South America, Central America, the Caribbean and the Pacific Islands with Zika infections.  The Centers for Disease Control and Prevention reports 50 laboratory-confirmed cases among U.S. travelers from December 2015- February 5, 2016.   As spring and summer approach, bringing with them larger and more active mosquito populations, we must be fully prepared to mitigate and quickly address local transmission within the continental U.S., particularly in the Southern United States.

The requested resources will build on our ongoing preparedness efforts and will support essential strategies to combat this virus, such as rapidly expanding mosquito control programs; accelerating vaccine research and diagnostic development; enabling the testing and procurement of vaccines and diagnostics; educating health care providers, pregnant women and their partners; improving epidemiology and expanding laboratory and diagnostic testing capacity; improving health services and supports for low-income pregnant women, and enhancing the ability of Zika-affected countries to better combat mosquitoes and control transmission. 

There is much that we do not yet know about Zika and its relationship to the poor health outcomes that are being reported in Zika-affected areas. We must work aggressively to investigate these outbreaks, and mitigate, to the best extent possible, the spread of the virus. Congressional action on the Administration’s request will accelerate our ability to prevent, detect and respond to the Zika virus and bolster our ability to reduce the potential for future infectious disease outbreaks.

Department of Health and Human Services - $1.48 billion

Centers for Disease Control and Prevention - $828 million.  The request includes funding to support prevention and response strategies through the following activities:

·         Support Zika virus readiness and response capacity in States and territories with mosquito populations that are known to transmit Zika virus, with a priority focus on areas with ongoing Zika transmission;

·         Enhance mosquito control programs through enhanced laboratory, epidemiology and surveillance capacity in at-risk areas to reduce the opportunities for Zika transmission;

·         Establish rapid response teams to limit potential clusters of Zika virus in the United States;

·         Improve laboratory capacity and infrastructure to test for Zika virus and other infectious diseases;

·         Implement surveillance efforts to track Zika virus in communities and in mosquitoes;

·         Deploy targeted prevention and education strategies with key populations, including pregnant women, their partners, and health care professionals;

·         Expand the CDC Pregnancy Risk Assessment Monitoring System, improve Guillain Barré syndrome tracking, and ensure the ability of birth defect registries across the country to detect risks related to Zika;

·         Increase research into the link between Zika virus infections and the birth defect microcephaly and measure changes in incidence rates over time;

·         Enhance international capacity for virus surveillance, expand the Field Epidemiology Training program, laboratory testing, health care provider training, and vector surveillance and control in countries at highest risk of Zika virus outbreaks; and

·         Improve diagnostics for Zika virus, including advanced methods to refine tests, and support advanced developments for vector control.


Centers for Medicare and Medicaid Services – $250 million. The request seeks a temporary one-year increase in Puerto Rico’s Medicaid Federal Medical Assistance Percentage (FMAP) to provide an estimated $250 million in additional Federal assistance to support health services for pregnant women at risk of infection or diagnosed with Zika virus and for children with microcephaly, and other health care costs.  This request does not make any changes to Puerto Rico’s underlying Medicaid program, and the additional funding will not be counted towards Puerto Rico’s current Medicaid allotment. Puerto Rico is experiencing ongoing active transmission of Zika. Unlike States, Puerto Rico’s Medicaid funding is capped, which has limited capacity to respond to these emergent and growing health needs.

Vaccine Research and Diagnostic Development & Procurement – $200 million. The request includes $200 million for research, rapid advanced development and commercialization of new vaccines and diagnostic tests for Zika virus. It includes funding for the National Institutes of Health to build upon existing resources and work to develop a vaccine for Zika virus and the chikungunya virus, which is spread by the same type of mosquito.  Funding will accelerate this work and improve scientific understanding of the disease to inform the development of additional tools to combat it. The request also includes resources for the Food and Drug Administration to support Zika virus medical product development including the next generation diagnostic devices.


Other HHS Response Activities – $210 million.  The request includes funding to establish a new Urgent and Emerging Threat Fund to address Zika virus and other outbreaks.  This funding would be available to support emerging needs related to Zika, including additional support to States for emerging public health response needs should mosquito populations known to be potential Zika carriers migrate to additional States.

In addition, the request includes funding to support Puerto Rico’s community health centers in preventing, screening, and treating the Zika virus, expand home visiting services targeting low-income pregnant women at risk of Zika virus, and provide targeted maternal and child health.

U.S. Agency for International Development - $335 million

The request includes investments to support affected countries’ ability to control mosquitoes and the transmission of the virus; support maternal health; expand public education on prevention and response; and create new incentives for the development of vaccines and diagnostics.  The request would also provide flexibility in the use of remaining USAID Ebola funds.  Activities would focus particularly on South America, Central America, the Caribbean, and would:

·         Implement integrated vector management activities in countries at-risk of Zika virus;

·         Stimulate private sector research and development of vaccines, diagnostics, and vector control innovations through public private partnerships and mechanisms to provide incentives such as advance market commitments or volume guarantees;

·         Support training of health care workers in affected countries, including providing information about best practices for supporting children with microcephaly;

·         Support for pregnant women’s health, including helping them access repellant to protect against mosquitos.

·         Establish education campaigns to empower communities in affected countries to take actions to protect themselves from Zika Virus as well as other mosquito-borne diseases; and

·         Issue a Global Health Security Grand Challenge calling for groundbreaking innovations in diagnostics, vector control, personal protection, community engagement and surveillance for Zika and other infectious diseases.

U.S. Department of State - $41 million

The funding request includes support for U.S. citizens in affected countries, medical support for State Department employees in affected countries, public diplomacy, communications, and other operations activities.  State would also support the World Health Organization and its regional arm, the Pan American Health Organization (PAHO), to minimize the Zika threat in affected countries while reducing the risk of further spreading the virus.  These resources will support critical public health actions underway, including preparedness, surveillance, data collection, and risk communication.  Activities would also include support for UNICEF’s Zika response efforts in Brazil; activities to bolster diagnostic capabilities through deployment of equipment and specialized training.

For more information on the Zika virus and CDC guidance about how Americans can protect themselves, visit http://www.cdc.gov/zika/


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Antimicrobial Properties of Peptides Derived from Reptiles

American alligator derived peptide, AM-CATH28,  combats Pseudomonas aeruginosa and multi-drug resistant Acinetobacter baumannii

New research presented at the 2016 ASM Biodefense and Emerging Diseases Research Meeting shows that a peptide produced by the American alligator (Alligator mississippiensis), AM-CATH28, has strong antimicrobial activity against gram-negative bacteria.  AM-CATH28, which is helical in structure and disrupts the bacterial membrane, has displayed antimicrobial activity against Pseudomonas aeruginosa and multi-drug resistant Acinetobacter baumannii.

“Drug resistance in bacteria has been increasing for the past several decades, and we’re now coming to a medical crisis in which we will no longer be able to treat common infections,” said Stephanie Barksdale, researcher in the van Hoek Lab, George Mason University.

Some antimicrobial peptides are already used clinically, such as colistin and vancomycin. Cathelicidin antimicrobial peptides are a class of peptide found in many animals, which has many effects, including strengthening the animal’s immune system, directly killing invading bacteria, or causing the bacteria to be less pathogenic.

American alligator derived peptide, Apo6, is antibacterial against biological threat agent Francisella

Researchers have identified a novel antimicrobial peptide in alligator blood plasma, Apo6, which exerts strong and rapid antimicrobial activity against both gram-negative and gram-positive bacteria. Apo6 can kill Francisella tularensis bacteria, which causes the disease tularemia and is considered a biological threat agent.

alligator Apo6“We found that Apo6 is able to kill Francisella bacteria by forming pores in their membrane,” said Dr. Monique van Hoek, Professor in the School of Systems Biology, George Mason University, “We also showed how the antimicrobial peptide Apo6 disturbs the membrane of the bacteria by observing the treated bacteria with scanning electron microscopy.”

American alligators (Alligator mississippiensis) make antimicrobial peptides as part of their innate immune system, the first line of immune defense that is shared by most higher-organisms. Antimicrobial peptides are small positively-charged peptides that can have both a host defense role and may exert a direct antimicrobial effect on bacteria.

The Apo6 peptide severely damages the membrane of F. novicida and disrupts the cell, which eventually leads to the death of the bacteria. Apo6 treatment was able to significantly increase the survival of Francisella-infected A549 cells and was able to prolong the survival of Francisella infected wax-worm larvae, an invertebrate infection model. (image credit: Dr. Kent Vleit, University of Florida).

Komodo Dragon-inspired Peptide Drgn-1 Promotes Clearance and Healing of Polymicrobial Biofilm-infected Wounds

New research has identified a histone H1-derived peptide from the Komodo dragon (Varanus komodoensis), called VK25, which could be used as a cationic antimicrobial peptide (CAMP). Using this peptide as inspiration, researchers designed a synthetic peptide DRGN-1, which contains two reversed amino acids at the N-terminus from the original protein sequence (VK25), and evaluated the antimicrobial and anti-biofilm activity of both peptides against P. aeruginosa and S. aureus. DRGN-1, but not VK25, exhibited potent antimicrobial and anti-biofilm activity, permeabilized bacterial membranes, and bound to DNA.

komodo dragon“Interestingly, wound healing was significantly enhanced by DRGN-1 in both uninfected and mixed biofilm (P. aeruginosa and S. aureus)-infected murine wounds,” said  Dr. van Hoek.

In a scratch wound closure assay used to elucidate the wound healing mechanism, the peptide promoted migration of HEKa keratinocyte cells, which was inhibited by mitomycin C (proliferation inhibitor) and AG1478 (EGFR inhibitor). DRGN-1 also trans-activated the EGFR-STAT1/3 pathway. Thus, DRGN-1 is a strong candidate for development as an alternative to antibiotics, especially for mediating the innate immune response and promoting wound healing. (image: komodo dragon, credit: Dr. Kent Vleit, University of Florida)

Starving Yourself Just Might Let You Live Longer and Healthier

While it is generally thought that bacteria are bad for us, research has shown that bacteria are important in our health and possibly longevity. Bacteria inhabit just about every part of the human body ranging from the skin, nose and the intestinal tract. In fact, bacteria make up more cells in the body than human cells and are collectively known as the microbiome. The microbiome of the intestine has been shown to play a role in disease such as obesity and diabetes. The intestinal microbiota has also been linked to a variety of beneficial functions that include the breakdown of nutrients, vitamin production and development of the immune system. For over 50 years, research has shown that reducing the amount of food an animal consumes (a process known as calorie restriction, CR) increases lifespan by retarding aging because most age-related diseases are delayed or reduced by CR.  Because diet and age can exert major effects on the composition of the intestinal microbiota, we hypothesized that CR, specifically 40% restriction, would delay/prevent age related changes in the intestinal microbiota.

Researchers from the University of Oklahoma Health Sciences Center (OUHSC) and the Missouri Mutant Mouse Resource and Research Center (MU MMRRC) studied the effect of age and life-long CR on the composition of the intestinal microbiota of young and old laboratory mice. The results will be presented at the ASM Microbe in Boston, Massachusetts on Saturday June 18, 2016.

As mice age, significant changes in the composition of the microbiota were observed. For example, there was a decrease or absence of specific bacteria in the old mice that were present in the young mice.  Conversely, there were also bacteria that were found in the old mice but not in the young mice. In addition to the changes described above, overall, there was about a 30% reduction in the number of different types of bacteria found in the old mice compared to the young mice.

CR altered the overall composition of the intestinal microbiota of old mice in comparison to their old counterparts that were given unlimited access to food. The old calorie restricted mice contained a microbiome profile that was highly similar to that found in the young mice.  Additionally, with the old calorie restricted mice there were no age-related reductions in the number of different types of bacteria and were comparable to that of the young mice.

From this study, researchers were able to demonstrate for the first time that CR prevented the age-related changes in the intestinal microbiome. The implications of this data suggests that the preservation of the young intestinal microbiota profile found within old CR mice may play a role in the prevention or delay of age-related diseases as well as the extension in lifespan seen with CR.  Additional research will be needed to determine if these differences in the microbiome are beneficial or harmful as well as determine whether or not these changes play a role in the extension of lifespan.

This study will be presented on at the American Society for Microbiology’s Microbe 2016 meeting in Boston, MA.

Medical Surge Capacity in the National Capital Region: Modeling a Pneumonic Plague Bioterror Event

New research presented at the 2016 ASM Biodefense and Emerging Diseases Research Meeting shows that the Washington, DC National Capital Region (NCR) may be limited in its capacity to provide medical care to all potential victims of a large-scale bioterror event. The findings of this study highlight the need to invest in regional health care coalitions to optimize patient distribution and use of resources during a surge event and to maintain and strengthen other regional and Federal resources for emergency public health response.

“While bioterror events are extremely rare occurrences nationally and globally, it is important to raise awareness regarding the limitations in local capacity to respond to biological threats, whether that be from a bioweapon or, more likely, from a naturally occurring threat such as a viral hemorrhagic fever or pandemic influenza,” said study author, Michael DeLuca, MS, Georgetown University School of Medicine. Michael DeLuca, MS, of Georgetown University School of Medicine and a Policy Fellow at Health Security Partners, an emerging thought leader on public health and national security.

Specifically, this study demonstrated a large deficit in the number of acute care beds available in the NCR in the first six days to treat the thousands of ill that may result from a successful attack on the area’s public transport system with pneumonic plague.

There is limited publicly available data on the ability of the NCR to respond to a significant biological event. This study examined the medical surge capacity of the NCR by modeling a hypothetical biological terror attack with pneumonic plague (Yersinia pestis) in the area’s metro system.

Medical care demand was estimated using Washington Metropolitan Area Transit Authority ridership data, publicly available data on disease attack rate, infectious dose, reproductive number, incubation period, and clinical severity. This data was used to estimate the total number of exposed and infected persons. The number of available acute care beds in the NCR was calculated using a variety of sources, including the DC Hospital Association utilization and occupancy rate data; Maryland Healthcare Commission, Virginia Health Information, Virginia Department of Health, and data obtained directly from hospital websites. The gap between needed and available beds during the first six days of disease spread, resulting from both primary and secondary infections, was then estimated.