Genome analysis following a national increase in Scarlet Fever in England 2014

Abstract

BackgroundDuring a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1st April 2014 to 18th June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics.Results555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95%CI 37.5–48.5; 14.7% higher than the percentage of emm3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS (p < 0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a “meta-ssa” phage defined by the presence of :315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360.vir phage was not detected yet the HKU360.ssa phage was present in 43/63 emm12 isolates but not found to be over-represented in isolates from patients with SF.ConclusionsThere is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3603-z) contains supplementary material, which is available to authorized users.

Managing scarlet fever

“…In England and Wales, the incidence of scarlet fever reduced from 250 notifications in 100,000 population per year in 1944 to less than 5 in 100,000 population per year in the 2000s 3 . There was a marked increase in 2013-2014 season to 25 notifications in 100,000 3 .…”

Managing scarlet fever

“…In England and Wales, the incidence of scarlet fever reduced from 250 notifications in 100 000 population per year in 1944 to less than 5 in 100 000 in the 2000s 3. In 2013-14, however, there were 25 notifications in 100 000 3.…”

“…In 2013-14, however, there were 25 notifications in 100 000 3. Around 87% of cases were in children under 10 2…”

“…It was associated with high levels of morbidity and mortality when epidemics were common in the 18th and 19th centuries in Europe and the USA 1. Although the disease nearly disappeared during the 20th century, several countries, including the UK, have recently experienced a re-emergence of scarlet fever 123. In this article, we discuss the management of scarlet fever.…”

Sunspot Cycle Minima and Pandemics: The Case for Vigilance?

“…Although factors such as herd immunity are widely suggested for the long-term oscillations of incidence an alternative explanation would be the episodic variability of the genome of the causative bacterial population Streptococcus pyogenes. S. pyogenes DNA was amplified by Chalker et al [12] with primers specific to particular emm genes and a spread of emm types were revealed in several districts of the UK. The sudden increase in virulence (from 2011 onward) was clearly not linked to emm type of the S. pyogenesbacillus, although in some investigations a dominance of emm99 seems to have been recorded in the UK [13].…”