Rapid epidemiological characterisation of a Streptococcus pyogenes outbreak using nanopore whole-genome sequencing

Streptococcus pyogenes, also known as Group A Streptococcus (GAS), is a gram-positive bacteria, often implicated in minor ailments such as sore throats, tonsillitis, and scarlet fever¹. However, infection with GAS can occasionally lead to life-threatening illnesses such as streptococcal toxic shock syndrome or necrotising fasciitis¹, and in such cases is referred to as invasive GAS. GAS is susceptible to antibiotics, but treatment must be administered rapidly to avoid potentially severe complications or death; GAS infections are responsible for more than 500,000 deaths worldwide every year1. Ongoing surveillance of GAS is essential to limit the spread of infection; this is especially important for outbreaks among children, as they represent a high-risk group. Rapid characterisation of circulating strains is crucial for early recognition, reporting and prompt treatments.

A higher than usual number of cases of GAS were recorded in England between 2022 and 2023 (figure 1)², with 4,622 notifications during this period, compared to an average of 1,294 notifications over the same period in the previous five years³. This resulted in a higher number of cases of invasive GAS and 30 children lost their lives as a result. As it was not clear whether this outbreak was the result of a particularly invasive strain of GAS, Alcolea-Medina et al. characterised the epidemiology of this outbreak using nanopore whole-genome sequencing². For two weeks from the day the UKHSA announced the outbreak (06 December 2023), they collected and then sequenced all invasive and non-invasive GAS isolates along with routinely collected clinical data. Isolates were prepared for nanopore sequencing with the Rapid Barcoding Kit and sequenced on R9.4.1 MinION Flow Cells on a GridION device. Genome assembly was performed with Flye⁴, followed by polishing with medaka⁵.

Of the 56 sequenced research samples, 10 were invasive isolates from blood cultures and other normally sterile sites, and 46 were non-invasive, mostly from surface wound and throat swabs. Nanopore sequencing identified the known virulence factors including emm genotypes, which encode the surface M protein used for strain typing, and 11 superantigen genes. As has been previously reported, the nanopore sequencing data confirmed that invasive isolates were more likely to carry the emm¹ genotype and belong to the emerging M1uk variant, but the novel finding revealed by multi-variable analysis was an association between serious invasive disease and the superantigen genes spea and spej (streptococcal pyrogenic exotoxin A and J), and not the emm1 gene or the M1uk clone.

Sequencing results were made available within three weeks at the peak of the epidemic, rather than retrospectively, highlighting the powerful impact that nanopore sequencing can have to provide rapid access to data during an ongoing outbreak when embedded in routine laboratories. The ability to rapidly produce genomic epidemiology data close to the sample source improves surveillance and informs public health measures.

In addition, nanopore sequencing at the sample source allows the linking of pathogen genotypes with routinely collected epidemiological data and the distinctive presentation of serious disease; data on genotype-phenotype correlation can be lost when molecular analysis is performed later and away from the sample source. This provides detailed information on potential molecular markers to better understand the pathogen and, potentially, the underlying mechanisms of serious disease. These insights also contribute to the future potential for the development of novel therapeutic and preventative interventions.

The authors pointed out that their findings may not be representative of the outbreak at a national level, as they only had access to isolates from their hospital network. Data from research samples collected from other hospitals would be needed to increase confidence in this novel link between specific virulence factors and invasive disease. This highlights how integrating nanopore isolate sequencing capability in routine laboratories would enable decentralised generation of genomic epidemiology data for such emerging community infections and to investigate hospital outbreaks with antimicrobial-resistant organisms. They concluded that local nanopore pathogen sequencing provides a way forward ‘allowing rapid outbreak investigation to inform clinical and public health teams’.

Conflicts of interest statement: Jonathan Edgeworth holds a part-time employment contract with Oxford Nanopore Technologies that commenced in October 2022. Guy's & St Thomas' NHS Foundation Trust signed a commercial collaboration agreement with Oxford Nanopore Technology in September 2022.