The story of a superbug from genome to advocacy

A ‘typhoid superbug’ in Pakistan has been in headlines around the world. Researchers identified a typhoid strain that has become resistant to multiple antibiotics. Elizabeth Klemm, one of those researchers, tells the story behind the headlines.

Young person drinking water from a tap in Pakistan

Credit: UK Department for International Development

The typhoid strain behind the outbreak in Pakistan has acquired an additional piece of DNA and so is resistant to multiple antibiotics.

The genetic structure of a strain of the bacteria that causes typhoid which is resistant to five classes of antibiotics has been uncovered by scientists at the Wellcome Sanger Institute with collaborators at Public Health England and Aga Khan University, Pakistan.

There is currently a major outbreak of this highly resistant typhoid fever in Pakistan, and there has been a single case in the UK following travel, which was isolated and treated.

This new study shows that the typhoid strain behind the outbreak has acquired an additional piece of DNA and so has become resistant to multiple antibiotics, including a third-generation antibiotic.

The results, published in mBio, suggest that treatment options are running out for typhoid, and there is an urgent need for more stringent preventative  strategies including vaccines.

Samples contained a plasmid we hadn’t seen in S. typhi before

I first heard about the typhoid outbreak in Pakistan at a conference in spring 2017. Clinicians presented their data and discussed how they were grappling with treating patients, who were mostly children.

Since Pakistan already had a lot of antibiotic-resistant typhoid, the preferred choice of treatment was ceftriaxone, a third-generation cephalosporin. But this new strain of Salmonella typhi was also resistant to ceftriaxone. Doctors were resorting to the few remaining drugs available, but these treatments were more complex and required hospitalisation in over half the cases.

It was clear to me that understanding the outbreak was very important, not just as a scientific exercise but also to alert the public to the growing concern of antibiotic resistance in typhoid and to accelerate a response to the outbreak.

The Pakistan groups asked our team at Sanger to perform genomic analysis, so I quickly set to work. The samples were rushed through sequencing and after an initial analysis I spotted something different about the outbreak samples – they contained a plasmid we hadn’t seen in S. typhi before.

The sequencing method we used had given us a fragmented version of the novel plasmid. We needed a high-quality ‘finished’ sequence of the whole plasmid.

I recruited some colleagues to help and they used a new sequencing platform called Oxford Nanopore MinION and sequenced the plasmid to completion in just a few hours. From there we identified the gene that conferred ceftriaxone resistance on the plasmid.

We compared this plasmid to other plasmids in published databases and found similar plasmid sequences reported all over the world, typically in E. coli.

We concluded that it was likely the plasmid was transferred from E. coli to the S. typhi that caused the outbreak. And since the S. typhi that picked up the plasmid already had several resistance genes hardwired into the chromosomal DNA, the effect was additive and explained why this strain was resistant to at least five antibiotics.

We classified this strain as ‘extensively drug-resistant’. This was significant because it marked the first largescale outbreak of typhoid with resistance levels this high – there had been a few isolated cases before but no persistent outbreak.

In the meantime, I had started a secondment at Wellcome

I was working on a project with the vaccines team to promote evidence for the impact vaccines can have on averting the development of antimicrobial resistance.

The idea is that if people get sick less in the first place, they won’t be taking as many drugs that drive the development of drug resistance. In addition, when pathogens acquire such high levels of drug resistance that they become harder to treat – as with the S. typhi in Pakistan – then preventing these infections with a vaccine is especially important.

The WHO SAGE group used this exact reasoning and cited the situation in Pakistan as part of the basis for their recommendation to pre-qualify a new typhoid vaccine.

Media coverage was an opportunity to advocate for the use of vaccines

Our study got picked up by the media, including Reuters and The Guardian, and got coverage around the world. It offered an opportunity to draw attention to the antibiotic resistance crisis and to advocate for the use of vaccines.

Seeing through this project from sequencing to advocacy, at Sanger and at Wellcome, has made me realise the impact basic science can have on global health. And I feel privileged to work at Sanger with so many talented bioinformaticians and with access to the latest technologies.