MICROBE 2018 recap - Tales of Biogas Core Microbial Communities: The Research, The Rant, The Learning Process

"Research is easy! You have your hypothesis, your starting point, experimentation, perhaps some optimizations and options you take along the way followed by results, analysis and whalah, you are done and have forever changed the world..."

... SAID NO ONE EVER!

Here's an example from a mathematical modeling of infectious disease class I took several years back while still in grad school.

The plan:

Everything goes smoothly...splendidly even, and we all take tea breaks as our analyses run seamlessly without errors or missing/wrongly formatted data leading to a totally understandible, interpretable results that confirms all our hypotheses...

Reality:

By the end, I think we all just wanted a stiff drink.

And this is research! 

The glory and terribleness of it - it's exciting, frustrating and above all a learning process.

MICROBE 2018 recap - Tiny Drivers of Evolution - HGT in Microbes

Dr. Michael Brockhurst, University of Sheffield
Causes and consequences of horizontal gene transfer (HGT) in microbes

We are now in the world of temperate phages...and one plasmid that we'll hear about later.

• Temperate phages have a two-stage life cycle, lytic and lysogenic (where they 'hide' by integrating in the genome and becoming a prophage).
• So what are the benefits of interacting and integrating temperate phages as a bacterium?
• Lots of horizontal gene transfer
• Accelerated evolutionary adaptation potential - how so?
• When you have phages jumping in and out of genomes leaving and taking DNA with them, you have the potential for mutational events and rearrangements...genes get turned on and off - this is all fuel for evolutionary adaptation (or just death, ya death can happen too).
• Increased competitiveness

Story Time...

MICROBE 2018 recap - Antibiotics and Evolution of Resistance - Poster Talk Take Home Messages

So another round of Poster Talks, this time on Antibiotic Resistance...let's boil these posters down to their take home messages and provide some links for further information!

Anna Seekatz - University of Michigan
Longitudinal impact of prophylactic antibiotic use on the gut microbiota and antimicrobial
resistance genes

Methods: 

• Use of cefazolin, clindamycin, vancomycin
• Up to 7 stool samples collected before and after antibiotic administration
• 16S rRNA gene sequencing
• qPCR to identify antibiotic resistance genes
• Mixed model analysis

THM: "While ultimately your gut microbiota does 'drift' away from itself over time, a short pulse of antibiotics DOES produce a discernable 'bump' in the population composition immediately following antibiotic administration"

Further Reading:

• Seekatz, Anna Maria, and Vincent Bensan Young. "Clostridium difficile Infection and the Tangled Web of Interactions Among Host, Pathogen, and Microbiota." Gastroenterology 154.6 (2018): 1573-1576.
• Francino, M. P. "Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances." Frontiers in microbiology 6 (2016): 1543.
• Shreiner, Andrew B., John Y. Kao, and Vincent B. Young. "The gut microbiome in health and in disease." Current opinion in gastroenterology 31.1 (2015): 69.
• Jakobsson, Hedvig E., et al. "Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome." PloS one 5.3 (2010): e9836.
• Raymond, Frédéric, et al. "The initial state of the human gut microbiome determines its reshaping by antibiotics." The ISME journal 10.3 (2016): 707.

MICROBE 2018 recap - Microbes that Know No Borders - Zoonoses and "One Health"

Welcome to Tanzania...land where most patients entering the hospital for fever are treated empirically for malaria and there is a poor clinical response to antimalarial drugs.

Why might patients have poor antimalarial response and high case fatality rates?

MICROBE 2018 recap - Microbes that Know No Borders - Emergence and Transmission

Dr. Julian Parkhill, Sanger Institute
Signatures of emergence and transmission in bacterial pathogens

Dr. Parkhill has been involved on analysis of transmission and emergence of pathogens for almost 2 decades now. A glance through his publication record shows involvement in epidemic analysis and antimicrobial resistance in Burkholderia, Campylobacter, Neisseria, Legionella, Cholera, Mycobacteria and has assisted in the development of tools and analysis for better visualization and annotation of sequence data, faster phylogenetic analysis, whole genome sequencing, SNPs and AMR, population structure and much more.

Today we looked at Extraintestinal Pathogenic E. coli (ExPEC) and Uropathogenic E. coli (UPEC), and once again we are looking at ST131 in particular as we did in the AMR Highlights blog.

• ST131 clones are said to have emerged in 2000, sequentially acquiring fluoroquinolone resistance followed by beta-lactam resistance (blaCTXM15), rapidly expanded and have remained stable ever since in terms of population size.

But is this really 'emergence'?

MICROBE 2018 recap - Microbes that Know No Borders - AMR, Humans and Animals

Dr. Susan Sanchez is from the College of Veterinary Medicine at the University of Georgia. She is the section head for Microbiology and Molecular Biology, the Assistant Director of the Biomedical Health Science Institute and the Chair of One Health.

Her research interests include: (i) Antimicrobial resistance (AMR) spread in humans and animals (ii) Staphylococcus and Salmonella with a focus on MRSA and (iii) Diagnostic testing for zoonses present in animals.

Her talk focused on how AMR spreads between humans and animals. Interestingly she started off by saying her adviser had said a long time ago that clinical microbiology is dead, we have antimicrobials. I think we can all agree, that is not true. Estimates suggest that a failure to address AMR could lead to 10 million deaths by 2050.

MICROBE 2018 - A moment to appreciate Art, Anecdotes, Imagination and Stress Poop...

Taking a brief break to appreciate the imaginative and artistic side of the ASM General meeting...

1990s-esk Viewmaster! 

The vendors were out in full force with creative ways of drawing in the crowd including video games where you shoot microbes, lots of spin the wheels, scavenger hunts followed by a claw game and of course throw backs to the childhoods of many of the attendees such as Karius...

There were plenty of buttons to collect throughout the conference as you made your way through the exhibition hall listening to poster talks, viewing posters and perusing vendors. You could easily establish your pen collection for the next year and giant microbes are always a staple in many of the vendor give aways (red blood cell via Eppendorf) and Chicken Pox via ATCC.

In the world of art both Trilobite Glassworks and Artologica were in attendance as well.

HIV magnet - Trilobite Glassworks

ComputerPhage - Trilobite Glassworks.
Also featured, several stickers courtesy of
ASM and other vendor booths

The computerphage by Trilobite Glassworks was made almost entirely of computer parts salvaged by her husband. Given my husband is a software engineer I thought he'd get a kick out of that.