It’s in the genes AKA Genetic determinants of AMR and where to find them

Written by Dr Sam Willcocks

Sam is Research Fellow at the London School of Hygiene & Tropical Medicine (LSHTM) investigating novel antimicrobials and virulence factors. Sam is also the lead for biological and pharmacological sciences within LSHTM’s AMR Centre. 

Listening to microbial genes requires something a bit more advanced than a sound bar but my, what stories they can tell.

We struggled to hear the first few notes, but we are now familiar with their melodies. And they are telling us all their secrets. We have made rapid advances in our technical ability to determine gene function, and we are using it to discover how bacteria resist antibiotics.

A starting approach is to hold up an earpiece to identify which genes are associated with AMR.

Perhaps if genes are a vinyl record then DNA sequencing is the gramophone. (I may have to abandon the metaphors early since I’m already in trouble and we still have a lot of ground to cover). Next Generation Sequencing, and, to some extent, DNA Microarrays and Polymerase Chain Reaction, allow us to directly compare the genomes, or parts of the genome, of drug-sensitive and drug-resistant strains and play spot-the-difference. It sounds painfully simple, but the applications are vast, particularly in the fields of diagnostics and epidemiology.

Genome-wide Association Studies allow us to track the spread of a resistant strain to identify where it originated from and where it is spreading to – and that can be at a global scale, or within a single hospital experiencing an outbreak.

A dawning reality is to be able to, at the point of care, rapidly identify the presence or absence of characteristic resistance genes from a pathogen causing disease in a patient. This will help the clinician to immediately place them on appropriate antibiotics to reduce the use of broad-spectrum or ineffective drugs that only feed the rise of AMR.

All well and good, but it’s not always just about which genes are present.

Often it is about which genes are being expressed, when, in what combination, and for how long. Enter mRNA technology – which tells us not which songs are in the library, but which are being played. Analysis of mRNA transcripts tell us which genes are activated (or repressed) in the presence of drug treatment. This is tantalising but carries a lot of noise. Try listening to Joni Mitchell whilst also playing Kanye West (that’s not so good either… definitely stop now with the music analogies).

More elegant is to screen for only the genes whose expression is absolutely required to survive antibiotic treatment. We achieve this by silencing each and every gene in the genome and then exposing the pathogen to the chosen antibiotic. If a silenced gene sensitises the bug to the drug, then we know it is crucial for resistance. Simples. This approach is made possible by methods such as RNA interference (RNAi), Transposon Sequencing (TnSeq), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology.

Acronyms Against Antimicrobial Resistance. AAAMR.

Knowing the resistance genes of a given pathogen against a given drug is useful in two major ways.

The first is that it informs us how the drug is acting – yes, we still don’t fully understand how many of the drugs we routinely consume actually work.

Secondly, it provides the chance of extending the useful life of existing drugs already in clinical use. If we know which genes a bacteria is using to resist a drug, and if we can target those genes with a second drug, we boost drug number one’s effectiveness by lowering resistance. Boom. Mic-drop.

Except not quite. We’re still going to need new drugs, no way around that.

We can screen natural compounds and synthetic derivatives until the cows come home, but pathogens will continually evolve resistance against them.

There is no greater selective pressure than ‘evolve or die.’

So what if we move the goal posts?

Don’t kill the pathogen. At least, not directly anyway. Think preventative measures such as vaccination and good hygiene and sanitation. Avenues like immunomodulation (regulation of the immune system); the use of competing ‘friendly’ bacteria; or antibacterial phage (viruses that kill bacteria) can all help to resolve infections without using microbicidal compounds. But for the purposes of this article, we’re interested in what the genes can tell us (and, wherever possible, tenuous music references).

So, beyond killing the pathogen, beyond even resistance genes, we come to the virulence genes. These are the genes required by a pathogen to survive in its host – in other words, required to make us sick. If we target these with the next generation of antimicrobials, we disarm but don’t kill the bacteria. Our immune system – always our best weapon against infection – can take care of the rest.

The genes are singing, and we just turned it up to eleven.