Governments are waking up to the dangers presented by antimicrobial resistance but the focus on clinical monitoring needs to be complemented with much more attention to livestock and wastewater contamination as potential sources of the next superbug, argues Neil Ward.
Communities around the world are threatened by rising antimicrobial resistance (AMR) levels. With infections from resistant pathogens already killing millions globally each year, the issue of AMR is approaching crisis point. Infants are particularly at risk; many common childhood antibiotics are now less than 50% effective, with familiar childhood infections like pneumonia, sepsis and meningitis becoming harder to treat.
In the UK specifically, the Government has hailed AMR as the next potential global pandemic. In England alone, 58,224 people had an antibioticresistant infection in 2022, up 4% from 2021. As available treatment options for bacterial, fungal and viral infections dwindle, public health bodies are looking for ways to preserve existing antimicrobial therapies and contain the spread of resistant infections.
Zoonotic diseases are the cause of many pandemics, yet funding for animal health agencies does not often allow for comprehensive monitoring of disease in livestock, pets and wildlife
Getting a handle on AMR must become a priority for all stakeholders. Understanding first where resistance is emerging, how it evolves, and how it spreads is central to preventing outbreaks – and genomic sequencing plays a critical role in understanding these factors. National biosurveillance programmes are essential in identifying emerging threats early and strategising a response. Clinical monitoring for AMR is commonplace, but with wastewater and livestock cited as a likely source of the next superbug, there are opportunities for governments to level up their approach to biosurveillance for greater insights.
Livestock tracking prevents pathogen spillover
Zoonotic diseases are the cause of many pandemics, yet funding for animal health agencies does not often allow for comprehensive monitoring of disease in livestock, pets and wildlife. More than 16 strains of bird flu have been identified in the UK, but only four are monitored extensively. Such gaps in monitoring bring a risk of pathogens spreading uncontained and undetected among animals. Left unchecked, pathogens could evolve and spillover into human populations, which is a significant risk as people and food animals are in regular and close contact.
By conducting ongoing genomic surveillance of food animals’ microbiomes as well as infectious diseases in livestock, resistant organisms that pose a threat can be identified. Having the genomic sequence for these pathogens allows further research to establish the mechanisms of resistance and gives the opportunity for intervention before pathogens make the jump to humans.
Governments are moving to expand the genomic characterisation and surveillance of pathogens affecting livestock. But AMR has no borders. Although we are going in the right direction, there is further benefit to gain from sharing screening data widely. Governments could have the deepest understanding of the microbial landscape of their region – but data sharing is essential in developing truly effective pandemic preparedness strategies and ensuring that early warning systems are in place globally.
Wastewater reveals pathogen and resistance in communities
It’s not just animals that are a potential source of AMR outbreaks. Misuse of antibiotics and environmental factors such as pollution are also known drivers of resistance in the general population. Wastewater surveillance using genomic sequencing is one useful strategy for tracking resistance rates of microbes circulating in populations locally.
While many countries recognise the value of wastewater analysis in early detection of disease outbreaks, accessing a more detailed understanding of the genetic characteristics of circulating pathogens is challenging. This is because the DNA in wastewater samples is often degraded or exists against a backdrop of other ‘noise’. As such, very high sequencing specificity and sensitivity are needed to get an accurate picture of the resistance traits of microbes in wastewater – and many countries lack access to such sequencing capabilities.
What is needed next is coordination across health, agriculture and environmental departments internationally
The latest sequencing technologies offer a solution to this challenge. Modern sequencing technologies, such as sequencing by binding, are up to 15 times more accurate than legacy methods, meaning they can be used to sample wastewater and detect new resistant strains early – acting as a litmus test for AMR in a region.
These data can help to portray a full picture of antimicrobial use and exposure and identify which antimicrobials may not be effective due to high local resistance. National bodies can use this knowledge to inform public health strategies and make sure patients aren’t being prescribed therapies that are unlikely to work.
Using genomic data for preventative response
Time is running out to prepare for the threat of AMR, and it is not something that can be achieved in isolation. Already, Europe has a high percentage of resistance to last-line antibiotics, such as carbapenems, yet just 16% of European Union member countries indicated that they still only collected AMR data at a local level and without a standardised approach. A consistent, global approach is needed. Databases that combine genomic and epidemiological information can reveal high-risk areas, identify global trends, and guide targeted action.
By expanding environmental surveillance capabilities and applying recent advances in sequencing technology, we can bring large-scale AMR surveillance networks to fruition. The cost of highly accurate sequencing has reduced significantly, while the number of samples that can be analysed has increased. What is needed next is coordination across health, agriculture and environmental departments internationally. This 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.
Neil Ward is vice president and general manager EMEA, PacBio, who has served as a key contributor to many of the world’s largest genomics projects including Genomics England’s 100,000 Genome Project, the Estonian Genome Project, and the whole genome sequencing of the 500,000 UK Biobank samples
