Streptococcal group A, C and G pharyngitis in school children: a prospective cohort study in Southern India

Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes

SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.

Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange

Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.

Global Streptococcus pyogenes strain diversity, disease associations, and implications for vaccine development: a systematic review

The high strain diversity of Streptococcus pyogenes serves as a major obstacle to vaccine development against this leading global pathogen. We did a systematic review of studies in PubMed, MEDLINE, and Embase that reported the global distribution of S pyogenes emm-types and emm-clusters from Jan 1, 1990, to Feb 23, 2023. 212 datasets were included from 55 countries, encompassing 74 468 bacterial isolates belonging to 211 emm-types. Globally, an inverse correlation was observed between strain diversity and the UNDP Human Development Index (HDI; r=-0·72; p<0·0001), which remained consistent upon subanalysis by global region and site of infection. Greater strain diversity was associated with a lower HDI, suggesting the role of social determinants in diseases caused by S pyogenes. We used a population-weighted analysis to adjust for the disproportionate number of epidemiological studies from high-income countries and identified 15 key representative isolates as vaccine targets. Strong strain type associations were observed between the site of infection (invasive, skin, and throat) and several streptococcal lineages. In conclusion, the development of a truly global vaccine to reduce the immense burden of diseases caused by S pyogenes should consider the multidimensional diversity of the pathogen, including its social and environmental context, and not merely its geographical distribution.

The global burden of sore throat and group A Streptococcus pharyngitis: A systematic review and meta-analysis

BACKGROUND

Contemporary data for the global burden of sore throat and group A Streptococcus (Strep A) pharyngitis are required to understand the frequency of disease and develop value propositions for Strep A vaccines.

METHODS

We used Clarivate Analytics' Web of Science platform to search WoS core collection, PubMed, Medline, data citation index, KCI-Korean Journal Database, Russian Science Citation Index, and the SciELO Citation Index for articles published between Jan 1, 2000, and Feb 15, 2021, from any country and in any language. The risk of bias was assessed using the JBI critical appraisal checklist. We used random-effects meta-analyses to pool sore throat and Strep A sore throat incidence rates from community-based studies. Our study was registered with PROSPERO (CRD42020181103).

FINDINGS

Of 5,529 articles identified by the search strategy, 26 studies met the inclusion criteria, but only two included data to determine incidence among adults. The pooled incidence rate, calculated for children only, was 82.2 episodes per 100 child-years (95% CI 25.2-286.3, I² = 100%) for sore throat (7 studies; 7,964 person years) and 22.1 episodes per 100 child-years (95% CI 14.7-33.1, I² = 98%) for Strep A sore throat (9 studies; 15,696 person years). The pooled cumulative incidence rate of sore throat from five studies was 31.9 per 100 children. There was significant methodological and statistical heterogeneity among studies, and five of 26 studies had a risk of bias score less than five (range: nine [maximum score] to one).

INTERPRETATION

Strep A sore throat has a considerable global burden. However, methodologically standardised studies are required to quantify that burden, analyse differences in rates between populations, and evaluate the likely impact of future Strep A vaccines.

FUNDING

This study was funded by Wellcome Trust 215,490/Z/19/Z.

Additive-Multiplicative Rates Model for Recurrent Event Data with Intermittently Observed Time-Dependent Covariates

Regression methods, including the proportional rates model and additive rates model, have been proposed to evaluate the effect of covariates on the risk of recurrent events. These two models have different assumptions on the form of the covariate effects. A more flexible model, the additive-multiplicative rates model, is considered to allow the covariates to have both additive and multiplicative effects on the marginal rate of recurrent event process. However, its use is limited to the cases where the time-dependent covariates are monitored continuously throughout the follow-up time. In practice, time-dependent covariates are often only measured intermittently, which renders the current estimation method for the additive-multiplicative rates model inapplicable. In this paper, we propose a semiparametric estimator for the regression coefficients of the additive-multiplicative rates model to allow intermittently observed time-dependent covariates. We present the simulation results for the comparison between the proposed method and the simple methods, including last covariate carried forward and linear interpolation, and apply the proposed method to an epidemiologic study aiming to evaluate the effect of time-varying streptococcal infections on the risk of pharyngitis among school children. The R package implementing the proposed method is available at www.github.com/TianmengL/rectime.

Additive rates model for recurrent event data with intermittently observed time-dependent covariates

Various regression methods have been proposed for analyzing recurrent event data. Among them, the semiparametric additive rates model is particularly appealing because the regression coefficients quantify the absolute difference in the occurrence rate of the recurrent events between different groups. Estimation of the additive rates model requires the values of time-dependent covariates being observed throughout the entire follow-up period. In practice, however, the time-dependent covariates are usually only measured at intermittent follow-up visits. In this paper, we propose to kernel smooth functions involving time-dependent covariates across subjects in the estimating function, as opposed to imputing individual covariate trajectories. Simulation studies show that the proposed method outperforms simple imputation methods. The proposed method is illustrated with data from an epidemiologic study of the effect of streptococcal infections on recurrent pharyngitis episodes.

Group C beta hemolytic Streptococci as a potential pathogen in patients presenting with an uncomplicated acute sore throat - a systematic literature review and meta-analysis

Objective: The pathogenicity of beta-hemolytic Streptococcus group C (GCS) in patients attending for an uncomplicated acute sore throat is unknown and it was the objective to clarify this.Design: Systematic literature review with meta-analysis. Setting Medline and Scopus were searched from inception to February 2019, with searches of reference lists, Subjects case-control studies stating prevalence of GCS in patients as well as healthy controls presented for children and adults separately. Studies including patients already treated with antibiotics and studies focused on patients with HIV, malignancy or immunosuppression were not included. Main outcome measures Pooled prevalence of GCS was compared between patients and controls using chi-square and was further explored by calculating the positive etiologic predictive value (P-EPV) showing the post-test probability of a link between a sore throat and the bacterial finding. P-EPV for GCS was compared with that for group A Streptococci (GAS) using figures from the same publications and patients.Results: Eleven studies were included. The prevalence of GCS among patients versus controls was similar in children (3.15 versus 2.87%, p = .44) but for adults higher in patients (11%) than in controls (5.6%) (p < .0001). The P-EPV for finding GCS in children with a sore throat was 9.3% (0.0-41%). The corresponding P-EPV for GCS in adults with a sore throat was 53% (36-67%) while the corresponding P-EPV for GAS in adults was 94% (90-96%).Conclusions: GCS do not seem associated with the uncomplicated acute sore throat in children but there is support for an association in adults being weaker than for GAS. A possible consequence is to ignore GCS in otherwise healthy patients at their first visit for an uncomplicated sore throat. This would enable a stronger focus on the use of modern point of care tests (POCTs) to detect GAS.Key pointsThere is no current consensus on the pathogenicity of group C beta-hemolytic Streptococcus (GCS) in patients attending for an uncomplicated acute sore throat.This systematic literature review concludes it is unlikely that GCS is involved in the uncomplicated sore throat in otherwise healthy children.This meta-analysis found a moderate link between GCS and the uncomplicated sore throat in adults.The link in adults between GCS and the sore throat is much weaker than the corresponding link for group A beta-hemolytic Streptococcus.