Comparative genome analysis of three Group A Streptococcus dysgalactiae subsp. equisimilis strains isolated in Japan

Introduction . Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a β-hemolytic streptococcus that causes severe invasive streptococcal infections, especially in the elderly and people with underlying diseases. SDSE strains are primarily characterized by Lancefield group G or C antigens. Hypothesis/Gap Statement. We have previously reported the prevalence of Lancefield group A SDSE (GA-SDSE) strains in Japan and have analysed the draft genome sequences of these strains. As GA-SDSE is a rare type of SDSE, only one complete genome has been sequenced to date. Aim. The present study is focused on genetic characteristics of GA-SDSE strains. In order to examine molecular characteristics, we also tested growth inhibition of other streptococci by GA-SDSE. Methodology. We determined the complete genome sequences of three GA-SDSE strains by two new generation sequencing systems (short-read and long-read sequencing data). Using the sequences, we also conducted a comparative analysis of GA-SDSE and group C/G SDSE strains. In addition, we tested multiplex and quantitative PCRs targeting the GA-SDSE, group G SDSE, and S. pyogenes . Results. We found a group-specific conserved region in GA-SDSE strains that is composed of genes encoding predicted anti-bacteriocin and streptococcal lantibiotic (Sal) proteins. Multiplex and quantitative PCRs targeting the GA-SDSE-specific region were able to distinguish between GA-SDSE, other SDSE, and S. pyogenes strains. The growth of GA-SDSE was suppressed in the presence of group G SDSE, indicating a possible explanation for the low frequency of isolation of GA-SDSE. Conclusion. The comparative genome analysis shows that the genome of GA-SDSE has a distinct arrangement, enabling the differentiation between S. pyogenes , GA-SDSE, and other SDSE strains using our PCR methods.

Impact of intra-partum Azithromycin on carriage of group A streptococcus in The Gambia: a posthoc analysis of a double-blind randomized placebo-controlled trial

BackgroundGroup A Streptococcus (GAS) is a major human pathogen and an important cause of maternal and neonatal sepsis.MethodsWe performed a posthoc analysis of a double-blind, placebo-controlled randomized-trial (ratio 1:1) carried out in The Gambia to determine the impact of one oral dose (2g) of intra-partum azithromycin on maternal and neonatal GAS carriage. Breast milk, nasopharyngeal and vaginal swabs were collected at different time points during 4 weeks post-treatment. All samples were processed using conventional microbiology techniques. Whole genome sequencing (WGS) of GAS isolates was performed by Illumina MiSeq platform.ResultsWe randomized 829 mothers who delivered 843 babies. GAS carriage in mothers in the azithromycin arm was lower in breast milk (0.28% vs 2.48%, Prevalence Ratio (PR)=0.11, 95% CI 0.01-0.90) and the nasopharynx (0.28% vs 1.93%, PR=0.15, 95% CI 0.02-1.19), but not in the vaginal tract (1.99% vs 1.93%, PR=1.03, 95% CI 0.37-2.91). Among neonates, GAS carriage in the nasopharynx was slightly lower in the azithromycin arm (0.57% vs 1.91%, PR=0.30, 95% CI 0.06-1.42). Prevalence of azithromycin-resistant GAS was similar in both arms, except for a higher prevalence in the vaginal tract among women in the azithromycin arm (1.99% vs 0.28%, PR=7.24, 95% CI 0.87-56.92). WGS revealed ten of the 45 GAS isolates (22.2%) were Streptococcus dysgalactiae subspecies equisimilis expressing Lancefield group A carbohydrate (SDSE(A)). All SDSE(A) isolates were azithromycin-resistant, harbouring macrolide resistant genes msrD and mefA.ConclusionsOral intra-partum azithromycin reduced prevalence of GAS carriage among mothers and neonates. Azithromycin-resistant SDSE(A) carriage was observed among participants treated with azithromycin.Short SummaryGroup A streptococcus (GAS) is an important cause of sepsis. One oral dose (2g) of intra-partum azithromycin reduced maternal and neonatal GAS carriage. However, azithromycin-resistant Streptococcus dysgalactiae subspecies equisimilis expressing Lancefield group A carbohydrate was detected in women receiving azithromycin.

Increasing macrolide resistance among Streptococcus agalactiae causing invasive disease in non-pregnant adults was driven by a single capsular-transformed lineage, Portugal, 2009 to 2015

We characterised Lancefield group B streptococcal (GBS) isolates causing invasive disease among non-pregnant adults in Portugal between 2009 and 2015. All isolates (n = 555) were serotyped, assigned to clonal complexes (CCs) by multilocus sequence typing and characterised by surface protein and pilus island gene profiling. Antimicrobial susceptibility was tested by disk diffusion and resistance genotypes identified by PCR. Overall, serotype Ia was most frequent in the population (31%), followed by serotypes Ib (24%) and V (18%). Serotype Ib increased significantly throughout the study period (p < 0.001) to become the most frequent serotype after 2013. More than 40% of isolates clustered in the CC1/alp3/PI-1+PI-2a genetic lineage, including most isolates of serotypes Ib (n = 110) and V (n = 65). Erythromycin and clindamycin resistance rates were 35% and 34%, respectively, both increasing from 2009 to 2015 (p < 0.010) and associated with CC1 and serotype Ib (p < 0.001). The Ib/CC1 lineage probably resulted from acquisition of the type Ib capsular operon in a single recombination event by a representative of the V/CC1 macrolide-resistant lineage. Expansion of the new serotype Ib/CC1 lineage resulted in increased macrolide resistance in GBS, causing invasive disease among adults in Portugal. The presence of this clone elsewhere may predict more widespread increase in resistance.

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

Diagnosing streptococcal pharyngitis in children on the basis of clinical appearance and throat culture is complicated by high colonisation rates and by the ability of other pathogens to cause clinically similar disease. To characterise the epidemiology of Lancefield Group A, C and G β-haemolytic streptococcus (GAS, GCS and GGS, respectively) in children, we conducted a 2-year prospective study of 307 school children between 7 and 11 years old. GGS and GAS were commonly identified organisms both for silent streptococcal colonisation and symptomatic sore throat, while GCS was uncommonly found. Streptococcal culture positivity at the time of clinical pharyngitis was estimated to reflect true streptococcal pharyngitis in only 26% of instances, with the frequency varying from 54% for children rarely colonised to 1% for children frequently colonised. Numerous GAS emm types were identified, including several types previously associated with severe pharyngitis (e.g. emm types 1, 3 and 28). No severe complications were seen in any child. These data suggest that the clinical diagnosis of streptococcal pharyngitis is likely to remain difficult and that treatment decisions will remain clouded by uncertainty. There remains a need for organism-specific rapid point-of-care streptococcal diagnostic tests and tests that can distinguish between streptococcal colonisation and disease.