Data platform reveals how antibiotic resistance spreads

The key to effective action against outbreaks of antibiotic-resistant bacteria is identifying the bacteria in good time and understanding how they spread. However, longer-term measures that interrupt the routes by which antibiotic resistance spreads require a detailed understanding of the many complex interfaces in the biological system linking humans, animals and the environment via which resistance is transmitted. Until just a few years ago, though, it was virtually impossible to systematically study and detect these transmission routes. This has changed now that it is possible to sequence the genomes of micro-organisms using whole genome sequencing (WGS). WGS is a technology that can rapidly deliver a complete and detailed breakdown of a microbe’s genetic information. This enables scientists to identify similarities in microbes’ genetic structures and thus to draw reliable conclusions on their development and how they spread between humans, animals and the environment.

Sharing data to identify links

Although human, veterinary and environmental laboratories routinely generate large volumes of WGS data, the scope for using them to monitor antibiotic resistance has as yet been limited by the need to collate and analyse data centrally. This is now possible thanks to a team of researchers led by Adrian Egli from the University Hospital of Basel, who have developed a new nationwide database – the Swiss Pathogen Surveillance Platform (www.spsp.ch).

They started by conducting a needs analysis with the various stakeholders that might supply data to the platform or use it. The researchers then used this as a basis for developing a solution that firstly accommodates heterogeneous user requirements and secondly is capable of processing the vast quantity of complex data from human, veterinary and environmental settings in a central location. Since this requires elaborate technical infrastructure and strong database and bioinformatics skills, the Swiss Pathogen Surveillance Platform is operated by the Swiss Institute for Bioinformatics (SIB). SIB project manager and bioinformatics specialist Aitana Lebrand has been responsible for the project for many years.

Legal issues resolved

Aside from the purely technical considerations, legal issues also proved to be a major challenge. This is because analyses intended to provide information on the spread of antibiotic resistance with implications for human medicine often have to use patient data. Such data, however, are particularly sensitive and subject to their own legal provisions. Nevertheless, by working with the authorities, ethics committees and the platform’s partners – including the Universities and University Hospitals of Basel, Bern, Geneva, Lausanne and Zurich and a large number of veterinary laboratories – the researchers were able to develop a regulatory and legal framework capable of delivering clearly regulated and efficient data collection, analysis and sharing processes.

The Swiss Pathogen Surveillance Platform was trialled with a small number of hospitals and a close focus on one resistant species of bacteria (methicillin-resistant Staphylococcus aureus or MRSA). The positive experience prompted Adrian Egli and his core team to substantially expand the number of users and scope of the platform. The Swiss Pathogen Surveillance Platform is now capable of providing all universities, university hospitals and veterinary medical centres in Switzerland with a standardised method of collecting and analysing genetic information for a large number of bacteria, viruses and fungi. A substantial number of cantonal hospitals and private laboratories are also connected to the system.

Basis for detailed antibiotic resistance monitoring

The platform demonstrated its fitness for purpose during the Covid-19 pandemic when it was used to share and analyse SARS-CoV-2 sequencing data, then promptly supply automated reports to the FOPH. To date, the genome sequences of some 135,000 SARS-CoV-2 isolates have been shared on the platform. SPSP is currently undergoing further development with numerous academic partners. In terms of antibiotic resistance, it provides an established basis that could be expanded to provide a much greater level of monitoring detail than is currently the case. The platform can also link to international surveillance networks because it already applies the relevant data standards. SPSP will require a mandate from the federal authorities if it is to continue to monitor antibiotic-resistant and virulent pathogens using WGS data going forward.

May 2022

Development of a Swiss surveillance database for molecular epidemiology of multi-drug resistant pathogens