Amid WHO’s Antimicrobial Resistance Awareness Week, wastewater sequencing and tracking pathogens in livestock are crucial to biosurveillance

This World Antimicrobial Resistance Awareness Week, global genomics expert Neil Ward of PacBio is calling for greater collaboration and sharing of genomic pathogen data to bolster preparation for future pandemics. His call to action follows the UK Health Security Agency’s announcement that 58,224 people in England had an antibiotic-resistant infection in 2022, up 4% on 2021. AMR is especially a growing problem in infants, with a recent study finding many common childhood antibiotics are now less than 50% effective due to the evolution of diseases such as pneumonia, sepsis, and meningitis. In order to respond rapidly to disease strains that have become resistant to antimicrobials, there is an increased need for highly accurate genomic sequencing in biosurveillance programs. Specifically, sequencing municipal wastewater samples and tracking pathogens circulating in livestock will create an early warning system by enabling scientists to monitor the spread of resistant pathogens through populations and across species before outbreaks become widespread.

“Post-Covid, countries and companies alike have realised that when it comes to pandemics, we’re all fighting the same fight, and we can’t do it in isolation. Wider sharing of genomic pathogen data will strengthen global biosurveillance, so scientists and officials can respond to potential threats while they are still localised and control outbreaks,” comments Ward. “Collaboration must also extend to non-healthcare bodies, such as government departments and private organisations in the agricultural space, like the UK’s Department for Environment, Food & Rural Affairs (DEFRA). These bodies play a critical role in disease surveillance considering that many pandemics have zoonotic origins. For example, more than 16 strains of bird flu have been identified in the UK, but only four are monitored extensively. Governments could vastly expand the genomic characterisation and surveillance of these pathogens if there was greater resourcing and inclusion of agricultural bodies in pandemic preparedness strategies.”

The generation of accurate genomic pathogen data has also been held back to date by limitations in sequencing technology. For example, while many countries recognise the value of wastewater analysis in early detection, the DNA in this sample type is often degraded and exists against a backdrop of other noise. As such, very high sequencing specificity and sensitivity are needed to get an accurate picture of pathogens – and many countries lack access to such sequencing capabilities. Scale has also been a challenge, with whole genome sequencing historically coming at a high price and with low throughput of samples. This has meant it hasn’t been feasible for many countries to maintain a surveillance programme that examines pathogens using highly accurate whole genome sequencing approaches.

“Recent advances in sequencing technology have opened up new opportunities to establish large scale disease surveillance networks. The cost of sequencing has reduced significantly, while the number of samples able to be analysed has increased. The latest sequencing technology also has extremely low error levels, with some methods, such as sequencing by binding, being up to 15 times more accurate than legacy methods,” continues Ward. “These leaps allow researchers to overcome existing cost and scale barriers, fuelling breakthroughs in our understanding of pathogens. Long term, international collaboration between health and agricultural organisations will underpin a shift towards a preventative approach to pandemics, where we recognise and respond to emerging public health red flags before they become crises.”

Case study

PacBio has collaborated with the UK’s National Collection of Type Cultures (NCTC) and the Wellcome Sanger Institute to whole genome sequence its collection of 3,000 historical bacterial strains. Producing high quality reference genomes for historical collections is vital for enabling researchers to what bacteria looked like before the advent of antibiotics, and how they have changed – including resistance traits. Neil Ward is a genomics industry veteran, currently VP and General Manager EMEA of sequencing firm PacBio. He has experienced first-hand the importance of international collaboration for genomics research, having served as a key contributor to many of the world’s largest genomics projects including the whole genome sequencing of the 500,000 UK Biobank samples, The Darwin Project, and the Estonian Genome Project.

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