Background
Group A
Streptococcus (GAS) is a major human pathogen, and infections caused by GAS are responsible for considerable global morbidity and mortality [
1]. The spectrum of infections caused by GAS ranges from non-invasive infections such as impetigo and pharyngitis, through to invasive infections such as necrotizing fasciitis and toxic shock syndrome. In addition, acute rheumatic fever (ARF) and its sequela, rheumatic heart disease (RHD) continue to represent a considerable disease burden in many settings. This includes New Zealand, where the incidence of ARF in Māori and Pacific children is amongst the highest in the developed world [
2].
At present, molecular typing of GAS is performed by sequence analysis of the 5’ hypervariable region of the
emm gene that encodes the M-protein [
3]. Recently, an
emm cluster-based typing system was proposed, which classifies existing
emm types into
emm clusters based on genetic relatedness of
emm protein sequences and functional activity of the M-protein [
4]. This cluster system is predictive of
emm pattern type, which, based on differential genotypic features and epidemiological associations, is a proposed marker for GAS tissue tropism [
4]. In general, pattern A-C strains are associated with GAS pharyngitis, pattern D strains with skin infections (particularly impetigo), and pattern E strains with both oropharyngeal and skin infections [
5].
In response to rising rates of ARF in New Zealand, the Rheumatic Fever Prevention Programme (RFPP) was set up by the New Zealand Ministry of Health. The RFPP is a multidisciplinary strategy aimed at reducing the incidence of ARF by two-thirds, to 1.4 cases per 100,000 population by June 2017 [
6]. A large part of this strategy is focused on primary prevention of ARF, through the timely diagnosis and treatment of GAS pharyngitis. One of the models of care within this programme is the provision of school-based sore throat management clinics, with these services targeted at children at highest risk of ARF [
6]. In New Zealand the distribution of ARF is unequal and those with the highest risk are Maori and Pacific and live in areas of low socio economic areas in the North Island [
2]. The Counties Manukau region (South Auckland, North Island) has the highest incidence of rheumatic fever and the highest number of school-based sore throat clinics.
Recent epidemiological analyses have demonstrated that approximately half of ARF-associated GAS strains in New Zealand fall into pattern D–i.e. strains classically associated with skin infections [
7]. Despite this association, and the high incidence of skin infections in New Zealand children [
8], there have been few studies in New Zealand describing the circulating GAS
emm types associated with superficial skin infections, and no contemporary studies comparing skin and pharyngeal isolates from high-risk children. In addition, it is not known whether there is any difference in GAS
emm types circulating amongst children at high risk of ARF, compared to children with minimal risk.
The Coalition to Accelerate New Vaccines Against Streptococcus (CANVAS) is an Australian and New Zealand GAS vaccine development programme that aims to identify suitable GAS vaccine candidates, with the long-term aim of preventing GAS-related disease, particularly ARF/RHD and invasive disease [
9]. At present, the most clinically advanced GAS vaccine candidates are those that target the N-terminal region of the M-protein, such as an experimental 30-valent M-protein vaccine [
10,
11]. One of the early aims of CANVAS is to define the global epidemiology of circulating GAS strains, in order to better inform vaccine development and putative vaccine coverage.
Accordingly, the aims of this study were to: (i) describe the GAS emm types, emm clusters and patterns from children at high risk of ARF with presumptive GAS pharyngitis or skin disease in a New Zealand setting, (ii) compare the emm types of GAS strains from children at high risk of ARF with those at low risk, and (iii) determine the theoretical coverage of the 30-valent M-protein vaccine candidate against contemporary GAS strains associated with pharyngitis or skin disease.
Discussion
This study describes the contemporary molecular epidemiology of GAS strains circulating amongst high-risk children in a setting with a high burden of ARF, compared with strains amongst children residing in the same country, with minimal risk of ARF [
2]. As expected,
emm pattern D, classically associated with skin tropism, predominated in GAS skin isolates in high-risk children accounting for approximately half of all
emm types. Somewhat surprisingly, approximately one-third of strains from high-risk children in Auckland with presumptive GAS pharyngitis also belonged to
emm pattern D. This is in marked contrast to the distribution observed in pharyngeal isolates from low-risk children in Dunedin, where pattern D strains comprised only 4 % of isolates. Though
emm pattern type has been described as an imperfect marker for tissue tropism [
5], the high prevalence of
emm pattern D strains observed in high-risk children in this study resembles observations in Aboriginal children in Australia, another Indigenous population with high ARF risk. A study in three remote Aboriginal communities found
emm pattern D strains accounted for 53 % of pyoderma isolates and 24 % of pharyngeal isolates [
16].
Clear differences were also observed in
emm cluster types between high-risk and low risk children in this study. The
emm clusters observed in pharyngeal isolates from low-risk Dunedin children closely resemble findings from other developed countries. [
17]. For example, Shulman et al., recently applied the
emm cluster system to pharyngitis isolates collected between 2000–2007 in the United States and found that clusters E4, A-C3 and A-C4 comprised 62.5 % of pharyngeal isolates, with isolates from cluster D4 representing <1 % of isolates [
17]. In our study, clusters E4, A-C3 and A-C4 comprised 79 % of pharyngeal isolates from Dunedin, but only 45 % of pharyngeal isolates from Auckland. Isolates from cluster D4 accounted for just 3 % of pharyngeal strains in low-risk Dunedin children in our study but 15 % of pharyngeal strains in high-risk Auckland children and were the most prevalent cluster amongst GAS skin isolates comprising 36 % of strains. The
emm-cluster D4 comprises 32
emm-types [
4], and was also the most prevalent cluster in a recent analysis of GAS isolates collected in Fiji where it accounted for over 30 % of strains [
18].
The high proportion of
emm pattern D and cluster D4 amongst GAS skin and pharyngeal isolates in Auckland (an area with the highest rates of ARF in New Zealand) is in keeping with recent work describing a high proportion of
emm pattern D and cluster D4 isolates amongst ARF-associated GAS strains in New Zealand [
7]. Taken together these observations add further weight to the hypothesis that skin infections may play an important etiological role in the pathogenesis of ARF [
7,
19]. Although the biological pathway is unclear, it is possible that colonizing GAS skin isolates may passage into the pharynx, or alternatively antecedent skin infection may ‘prime’ the immune system in an, as yet, uncharacterized manner, and contribute to the autoimmune process characteristic of ARF [
20].
Previous studies have shown the theoretical coverage of the 30-valent GAS vaccine is reduced in low-income countries where the diversity of
emm-types is highest [
21]. In this study, vaccine coverage has been compared between different populations within the same country. The theoretical coverage was low amongst isolates from high-risk Auckland children for which the Simpson’s index for strain diversity is high, although did increase when the putative effect of cross-opsonic antibodies was considered. However approximately 40 % of skin-associated isolates and 28 % of Auckland pharyngeal isolates have not yet been tested for potential cross-opsonic activity [
10,
11]. In contrast, the theoretical vaccine coverage for pharyngeal isolates from low-risk children in Dunedin is 93.2 % before taking into account the added potential effect of in vitro cross-opsonization. The high theoretical coverage in this low-risk population likely reflects the similarities in
emm-clusters observed with pharyngeal strains from the US [
17], as the 30-valent vaccine was designed to include
emm-types commonly associated with pharyngitis in North America [
10]. These findings demonstrate the importance of broad population sampling when assessing theoretical vaccine coverage.
There were a number of limitations with this study. It was assumed that GAS pharyngeal isolates were from children with pharyngitis, although information on clinical symptoms was not available for each child. Within the school-based programme, children are encouraged to present for assessment when they have a sore throat, though it remains possible that some of these isolates represent GAS colonization with concurrent viral pharyngitis, rather than true, serologically confirmed, GAS pharyngitis [
22]. Similarly, clinical information about each child who had a skin swab submitted for testing was not available. However, as these swabs were submitted as part of a primary care consultation, it is likely that the majority of children had clinical symptoms suggestive of a skin infection. Moreover, our sampling period was over a relatively short timeframe; previous work, including a study from New Zealand, has demonstrated temporal variation in the proportional distribution of GAS
emm types.
Acknowledgements
Not applicable.