Microbes don’t live in single-strain groups – they mingle. Antimicrobial resistance can be passed between strains as well as within them. What does this mean for the future of single-cell sequencing and the fight against AMR?
In part 3 of our feature series on antimicrobial resistance, we discuss the possibilities of sequencing mixed communities.
In this series so far, we have explored the Institute’s work on the rise of antimicrobial resistance (AMR) and how the Institute developed a cutting-edge single-cell genome analysis method giving a detailed picture of exactly how resistance genes are evolving in Salmonella.
Now we will take a look at what the future could hold for single cell sequencing and AMR. There are still many challenges ahead.
Historically, single-cell sequencing of microorganisms was generally done on somewhat artificial communities comprising a uniform strain of one species.
In reality, microbes are diverse and social creatures. Different strains and species have interactions with each other which are not well-understood, but we do know this includes passing genes back and forth - including those that offer resistance to antimicrobials.
By employing the latest single-cell sequencing technology, researchers at the Earlham Institute are hoping to generate unprecedented levels of cell-specific genetic information - offering new insights into how microorganisms interact with each other.
The first step is working out the best way to sequence mixed communities while retaining both clarity of analysis and high throughput.
Dr Chris Quince, High-Resolution Microbiomics Group Leader at the Earlham Institute and Quadram Institute, says single-cell sequencing of microbiomes is essential for fully understanding the transmission of AMR genes.
“A good example of where human activity is impacting the spread of AMR genes is in rivers,” he says. “Sewage discharged into rivers is both a source of AMR genes and antibiotics, even if it is treated, but much worse if it is not.”
“Sewage treatment is a high-energy process. A wide variety of microorganisms mix under conditions ideal for growth. Large quantities of gut microbes meet large quantities of environmental microbes in a way which would not generally occur in nature.
“It allows for a lot of gene exchange.”
Rivers often contain low levels of antibiotics through field run-off and sewage. As previous research from the Institute has demonstrated, low-dose exposure to an antimicrobial is less likely to kill microbes and helps to drive selection for resistance.
As a result, the sediment offers the perfect conditions for AMR to evolve and spread.
Dr Quince has published research on antibiotic consumption and its impact on AMR genes found in the gut microbiome with Dr Falk Hildebrand, Group Leader at the Earlham Institute and Quadram Institute.
They analysed 3096 microbiomes from healthy people not using antibiotics and compared resistance genes with reference genomes.
The work indicated use of antibiotics ramps up the number of resistance genes being passed back and forth between strains in a microbiome. And the genes spread so easily that the microbiome is influenced by national trends in antibiotic consumption - regardless of whether the individual has consumed them.
We need a much broader view of these communities. The gut is a very complex environment. We can test two gut species to see if they transmit AMR to each other, but we are putting them in an agar plate together. In the real world they may live in very different parts of the gut and never come in contact.
Chris Quince, Group Leader
Dr Quince says single-cell sequencing of raw samples offers possibilities for assessing spread through a mixed population of microbes. This approach could also be used on uncultured cells, which would limit the need for lab growth of cells before analysis.
“Some microbes may not be easy to culture in a lab,” he explains, “and being able to sequence them without culturing would make a difference.”
He also believes a mixed culture gives a clearer idea of which species to concentrate on when sequencing.
“We need a much broader view of these communities. The gut is a very complex environment.
“We can test two gut species to see if they transmit AMR to each other, but we are putting them in an agar plate together. In the real world they may live in very different parts of the gut and never come in contact.
“It’s not just about the possibility it could happen, it’s about assessing the real likelihood of transmission between two species.”
He explains antibiotic use does not just pressure pathogenic bacteria to evolve. It also puts pressure on harmless “friendly” microorganisms to develop AMR.
This response means our gut microbiomes may act as a reservoir for AMR genes to pass between pathogens. Therefore it is vital to look at interactions between species – including species that are not of concern in themselves.
Further research at the Earlham Institute is being conducted by Dr Rob James, who is conducting experiments to track the movement of AMR between pathogens and the beneficial microbes that are resident in the gut microbiome. He is working in collaboration with Dr Falk Hildebrand and Dr Naiara Bereza at the Quadram Institute.
“If we understand the process of acquisition better, then it could allow us to improve drug stewardship,” concludes Dr Quince.
The previous work involved a monoculture. Now we want to see if we can use it on a mixed community of bacteria and track microbial interactions within a microbiome. This could open up a lot of possibilities.
Yash Bancil, PhD Researcher
PhD student Yash Bancil is working in the Macauley Group to take the project forward, using samples provided by Drs James and Bereza.
He is deploying the same single-cell sequence approaches the Earlham Institute used to analyse AMR in Salmonella to study the rare microbial species found within a complex microbiome.
“The previous work involved a monoculture,” he explains. “Now we want to see if we can use it on a mixed community of bacteria and track microbial interactions within a microbiome. This could open up a lot of possibilities.”
Single-cell sequencing is a game-changer in genetics, detecting the genome, transcriptome, and other multi-omics of individual cells. It shows differences, evolutionary relationships, and small sub-populations - among other details - normally lost in traditional sequencing.
Associated genomic technologies continue to develop at pace, revealing the complexity of the cell types that make up multicellular life.
The Earlham Institute’s cutting-edge equipment and research offer pioneering and unique platforms for single-cell isolation and sequencing. Contact us for more information.
Read all the articles in our "single-cell sequencing and AMR" series below:
The rise in untreatable bacterial infections is one of the top 10 health threats currently facing humanity. In the first of a three-part series, we discover how the Earlham Institute is tackling this existential threat.
In our last article, we explored how low-level exposure to antibiotics in the environment is affecting the emergence of resistance genes in Salmonella. Here, we explore how single-cell genomics can elevate our understanding of how AMR arises - and equip us with the knowledge to tackle this existential threat.
