MICROBE 2018 recap - Jumping back into AMR for a moment...

As you can probably tell I attempted to hop into as many AMR sessions as possible as that is a primary interest of mine...

So before we finish off this blog series on some ancient infectious disease and microbial ecology (upcoming...) let's hop back in briefly to Dr. Lance Price's talk and hit some of his highlighted points.

Lance Price, George Washington University
Expanding our view of zoonotic pathogens: How genomics is revealing insidious host jumps and AMR transmissions

• So we've heard a lot about E. coli ST131 this meeting - it's broad host range, extensive resistance and wide geographic dispersal globally.
• So in thinking about these AMR pathogens spread particularly in E. coli were learn this a lot of overlap of these E. coli STs (isolates) within the meat market and clinic. They have their own clusters, but there is also overlap.
• Through phylogenetic analysis of different STs of E. coli we find both human and 'meat' clade ancestors suggesting independent host jumps.
• ST10 and ST38: ancestor in meat, yet found in clinical isolates
• ST12 found to have humans as the ancestor but has been found in food animal production isolates
• But it's not just limited to human <> meat...enter poultry, APEC and the ColV plasmid
• ST95 has a human ancestor, has been found in meat and isolates have been obtained from poultry falling into ST95 characterized as APEC (Avian Pathogenic E. coli). So there is potential for human isolates moving into poultry, acquiring plasmid then spilling back over into humans and meat.
• ST117 has been an emerging APEC problem in poultry but there is evidence of spillover into humans and in food production animals (meat) and is causing sporadic spread.

So policy? Given the expanding issue of these isolates many with AMR in our food animal production line... what is being done?

California has now restricted use of antibiotics in animals.
(the actual senate bill if you are interested, SB27)

• This is all good but in the event that these jumps have already occurred and establishment of these AMR strains has happened in humans. Legislation of this sort will have little effect.
• BUT it does have the potential, if followed long enough, for 'washing out' of sporadic spreaders.

From post about Canada's growing problem of antibiotic resistant bacteria being found in meat
and there being less food inspection agents. (https://eatinggreener.wordpress.com/tag/antibiotics/)

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 - 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 recap - AMR in the Americas, Highlights

Highlights from the Session:

Surveillance of Antibacterial Resistance in the Americas

Mariana Castanheira, JMI Laboratories and the SENTRY Program

• The SENTRY program was established in 1997 and is one of the longest running antimicrobial surveillance programs globally. Check out their website for more information and access to visualizations of their surveillance. One of the things I note is the obvious need for AMR surveillance in Africa and parts of the middle east where I see by their map much data is missing/lacking.
• Some major sequence types to keep a close eye on with respect to growing and expanding resistance in the Americas (especially Latin America) include E. coli ST131 and K. pneumoniae ST258.
• When interrogating genes for resistance in E. coli and K. pneumoniae it was found that diversity within resistance encoding genes was higher in E. coli than K. pneumoniae. 
• 0.5% of E. coli have been found resistant to Colistin
• 2.3% of K. pneumoniae have been found resistant to  Colistin
• mcr1 was found in E. coli while K. pneumoniae appeared to multiple mechanisms and genes involved conferring colistin resistance including mcr1, mrgB disruption or alteration, and pmrB.
• A. baumannii has show increasing resistance profiles within Latin America when 1997-2000 was compared to 2013-2016. Rises were seen in resistance to:
• Meropenem (18.4% to 86.3%) 
• Levofloxacin (76.9% to 87.6%)
• Amikacin (77.3% to 82.4%)
• Ampicillin-sulbactam (70.7% to 83.6%)
• Colistin (0.8% to 3.4%).
•  Of note: Susceptible and resistant isolates have been shown to have the same pattern of expression of their resistance encoding genes so you cannot use that as a marker of organisms 'resistance'.