Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections

The IgG-specific endoglycosidases EndoS and EndoS2 are distinguished by conformation and antibody recognition

The IgG-specific endoglycosidases EndoS and EndoS2 from Streptococcus pyogenes can remove conserved N-linked glycans present on the Fc region of host antibodies to inhibit Fc-mediated effector functions. These enzymes are therefore being investigated as therapeutics for suppressing unwanted immune activation, and have additional application as tools for antibody glycan remodeling. EndoS and EndoS2 differ in Fc glycan substrate specificity due to structural differences within their catalytic glycosyl hydrolase domains. However, a chimeric EndoS enzyme with a substituted glycosyl hydrolase from EndoS2 loses catalytic activity, despite high structural homology between the two enzymes, indicating either mechanistic divergence of EndoS and EndoS2, or improperly-formed domain interfaces in the chimeric enzyme. Here, we present the crystal structure of the EndoS2-IgG1 Fc complex determined to 3.0 Å resolution. Comparison of complexed and unliganded EndoS2 reveals relative reorientation of the glycosyl hydrolase, leucine-rich repeat and hybrid immunoglobulin domains. The conformation of the complexed EndoS2 enzyme is also different when compared to the earlier EndoS-IgG1 Fc complex, and results in distinct contact surfaces between the two enzymes and their Fc substrate. These findings indicate mechanistic divergence of EndoS2 and EndoS. It will be important to consider these differences in the design of IgG-specific enzymes, developed to enable customizable antibody glycosylation.

Enhanced bactericidal, antibiofilm and antioxidative response of Lawsonia inermis leaf extract synthesized ZnO NPs loaded with commercial antibiotic

Globally, antibiotic resistance is a challenging issue in healthcare sector. The emergence of multiple drug-resistant bacteria has forced us to modify existing medicines and or formulate newer medicines that are effective and inexpensive. In this perspective, this study involves the formation of zinc oxide nanoparticles (ZnO NPs) by utilizing the Lawsonia inermis (Li) leaf extract. The prepared L. inermis leaf extract mediated ZnO NPs (Li-ZnO NPs) were bio-physically characterized. The antibacterial and radical scavenging effects of Li-ZnO NPs were evaluated. In addition, ZnO NPs were conjugated with standard antibiotic (ciprofloxacin) and its drug loading efficiency, drug release and antibacterial efficacy were tested and compared with non-drug loaded ZnO NPs. An absorbance peak at 340 nm was noted for Li-ZnO NPs. After conjugation with the drug, two absorbance peaks- one at 242 nm characteristic of ciprofloxacin and the other at 350 nm characteristics of ZnO NPs were observed. The crystallite size was 18.7 nm as determined by XRD. The antibacterial effect was higher on Gram-positive (S. aureus and S. pyogenes) than the Gram-negative pathogens (E. coli and K. pneumoniae). Inhibition of S. aureus and S. pyogenes biofilm at 100 μg mL-1were, respectively, 97.5 and 92.6%. H2O2 free radicals was inhibited to 90% compared to the standard ascorbic acid at 100 μg mL-1. After drug loading, the FTIR spectrum confirmed the existence of ciprofloxacin peaks at 965 cm-1 and Zn-O bond at 492 cm-1. The drug loading capacity of 15 nm sized ZnO NPs was higher (58, 75, 90 and 95% at 1, 2.5, 5 and 10% drug concentrations, respectively) compared to 20 nm. Similarly, the percentage of drug (ciprofloxacin) released from 15 nm ZnO NPs were increased to 90% at 10% drug-loaded samples, respectively. Also, the antibiotic loaded ZnO NPs had significant antibacterial effects against tested bacteria compared to Li-ZnO NPs and ciprofloxacin alone. This revealed that the antibiotic loaded ZnO NPs offer a sustainable route to treat multi-drug-resistant bacterial infections.

Antimicrobial peptide-conjugated phage-mimicking nanoparticles exhibit potent bactericidal action against Streptococcus pyogenes in murine wound infection models

Streptococcus pyogenes is a causative agent for strep throat, impetigo, and more invasive diseases. The main reason for the treatment failure of streptococcal infections is increased antibiotic resistance. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been rising with a significant impact on public health and the veterinary industry. The development of antibiotic resistance and the resulting emergence of multidrug-resistant bacteria have become primary threats to the public health system, commonly leading to nosocomial infections. Many researchers have turned their focus to developing alternative classes of antibacterial agent based on various nanomaterials. We have developed an antibiotic-free nanoparticle system inspired by naturally occurring bacteriophages to fight antibiotic-resistant bacteria. Our phage-mimicking nanoparticles (PhaNPs) display structural mimicry of protein-turret distribution on the head structure of bacteriophages. By mimicking phages, we can take advantage of their evolutionary constant shape and high antibacterial activity while avoiding the immune reactions of the human body experienced by biologically derived phages. We describe the synthesis of hierarchically arranged core-shell nanoparticles, with a silica core conjugated with silver-coated gold nanospheres to which we have chemisorbed the synthetic antimicrobial peptide Syn-71 on the PhaNPs surface, and increased the rapidity of the antibacterial activity of the nanoparticles (PhaNP@Syn71). The antibacterial effect of the PhaNP@Syn71 was tested in vitro and in vivo in mouse wound infection models. In vitro, results showed a dose-dependent complete inhibition of bacterial growth (>99.99%). Cytocompatibility testing on HaCaT human skin keratinocytes showed minimal cytotoxicity of PhaNP@Syn71, being comparable to the vehicle cytotoxicity levels even at higher concentrations, thus proving that our design is biocompatible with human cells. There was a minimum cutoff dosage above which there was no evolution of resistance after prolonged exposure to sub-MIC dosages of PhaNP@Syn71. Application of PhaNP@Syn71 to a mouse wound infection model exhibited high biocompatibility in vivo while showing immediate stabilization of the wound size, and infection free wound healing. Our results suggest the robust utility of antimicrobial peptide-conjugated phage-mimicking nanoparticles as a highly effective antibacterial system that can combat bacterial infections consistently while avoiding the emergence of resistant bacterial strains.

Generation of green electricity from sludge using photo-stimulated bacterial consortium as a sustainable technology

Microbial fuel cell (MFC) is a bio-electrical energy generator that uses respiring microbes to transform organic matter present in sludge into electrical energy. The primary goal of this work was to introduce a new approach to the green electricity generation technology. In this context a total of 6 bacterial isolates were recovered from sludge samples collected from El-Sheikh Zayed water purification plant, Egypt, and screened for their electrogenic potential. The most promising isolates were identified according to 16S rRNA sequencing as Escherichia coli and Enterobacter cloacae, promising results were achieved on using them in consortium at optimized values of pH (7.5), temperature (30°C) and substrate (glucose/pyruvate 1%). Low level red laser (λ = 632.8nm, 8mW) was utilized to promote the electrogenic efficiency of the bacterial consortium, maximum growth was attained at 210 sec exposure interval. In an application of adding standard inoculum (107 cfu/mL) of the photo-stimulated bacterial consortium to sludge based MFC a significant increase in the output potential difference values were recorded, the electricity generation was maintained by regular supply of external substrate. These results demonstrate the future development of the dual role of MFCs in renewable energy production and sludge recycling.

Chemical Composition of the Cinnamomum malabatrum Leaf Essential Oil and Analysis of Its Antioxidant, Enzyme Inhibitory and Antibacterial Activities

Cinnamomum species are a group of plants belonging to the Lauraceae family. These plants are predominantly used as spices in various food preparations and other culinary purposes. Furthermore, these plants are attributed to having cosmetic and pharmacological potential. Cinnamomum malabatrum (Burm. f.) J. Presl is an underexplored plant in the Cinnamomum genus. The present study evaluated the chemical composition by a GC-MS analysis and antioxidant properties of the essential oil from C. malabatrum (CMEO). Further, the pharmacological effects were determined as radical quenching, enzyme inhibition and antibacterial activity. The results of the GC-MS analysis indicated the presence of 38.26 % of linalool and 12.43% of caryophyllene in the essential oil. Furthermore, the benzyl benzoate (9.60%), eugenol (8.75%), cinnamaldehyde (7.01%) and humulene (5.32%) were also present in the essential oil. The antioxidant activity was indicated by radical quenching properties, ferric-reducing potential and lipid peroxidation inhibition ex vivo. Further, the enzyme-inhibitory potential was confirmed against the enzymes involved in diabetes and diabetic complications. The results also indicated the antibacterial activity of these essential oils against different Gram-positive and Gram-negative bacteria. The disc diffusion method and minimum inhibitory concentration analysis revealed a higher antibacterial potential for C. malabatrum essential oil. Overall, the results identified the predominant chemical compounds of C. malabatrum essential oil and its biological and pharmacological effects.

Prevalence, Antibiotic Susceptibility Profile and Associated Factors of Group A Streptococcal pharyngitis Among Pediatric Patients with Acute Pharyngitis in Gondar, Northwest Ethiopia

Background

Streptococcus pyogenes (S. pyogenes) or group A streptococcus is a common cause of bacterial pharyngitis in children. Since it is difficult to distinguish between viral and bacterial pharyngitis using solely signs and symptoms, culture-based diagnosis and treatment are critical for avoiding serious complications. Therefore, this study aimed to determine the prevalence, antimicrobial susceptibility patterns, and associated factors of S. pyogenes among pediatric patients with acute pharyngitis.

Methods

A hospital-based cross-sectional study was conducted at the University of Gondar Comprehensive Specialized Hospital from April to June 2021. Standard microbiological procedures were used to collect and process throat swabs and to isolate and identify S. pyogenes. The disc diffusion method was used for antimicrobial susceptibility testing (AST).

Results

A total of 215 children with acute pharyngitis were included in this study. Of these, 23 (10.7%) were culture positive for S. pyogenes. The presence of an inflamed tonsil, tonsillar exudate, scalariform rash, and dysphagia were associated with streptococcal pharyngitis. Children aged 5 to 15 were more susceptible to streptococcal throat infection than younger children. Penicillin, vancomycin, chloramphenicol, clindamycin, and ceftriaxone were effective against 100%, 95.7%, 95.7%, 91%, and 87% of isolates, respectively. In contrast, 56.5%, 39.1%, and 30.4% of isolates showed at least reduced susceptibility to tetracycline, erythromycin, and azithromycin, respectively.

Conclusion

Streptococcus pyogenes is responsible for 10.7% of acute pharyngitis cases among pediatric patients in the study area. Although all isolates remain sensitive to penicillin, many showed reduced susceptibility to tetracycline and macrolides. Therefore, prior to antibiotic prescription, screening children with acute pharyngitis for S. pyogenes and testing the antibiotic susceptibility of isolates is recommended.

Assessment of the Relationship between Clinical Manifestation and Pathogenic Potential of Streptococcus pyogenes Strains-Distribution of Genes and Genotypes of Toxins

Streptococcus pyogenes is one of the most important species among beta-haemolytic streptococci, causing human infections of different localization. It is isolated from clinical specimens relatively frequently. In this study, the frequency and co-occurrence of toxin genes (speA, speB, speC, speH, speJ, speK) among 147 S. pyogenes strains were evaluated, using real-time PCR. In addition, the relationship between the occurrence of these genes and the origin of S. pyogenes strains from selected clinical material was assessed. The speB gene was present with the highest incidence (98.6%), while the speK gene was the least frequent (8.2%) among the tested strains. Based on the presence of the detected genes, the distribution of 17 genotypes was determined. The most common (21.8%), was speA (−) speB (+) speC (−) speH (−) speJ (−) speK (−) genotype. Furthermore, significant variation in the presence of some genes and genotypes of toxins in S. pyogenes strains isolated from different types of clinical material was found. There is a considerable variety and disproportion between the frequency of individual genes and genotypes of toxins in S. pyogenes strains. The relationship between the origin of S. pyogenes isolates and the presence of toxins genes indicates their pathogenic potential in the development of infections of selected localization.

In Silico Structural and Functional Analysis of Cold Shock Proteins in Pseudomonas fluorescens PF08 from Marine Fish

ABSTRACT

Pseudomonas fluorescens is a specific spoilage microorganism of refrigerated marine fish, and is highly adapted to low temperature. Cold shock proteins (CSPs) play an important role in cold adaptation of bacteria. In this study, CSP genes were identified from the genome of P. fluorescens PF08 by search of the conserved domain of CSPs with HMMER software, and the CSP physicochemical properties, structures, and functions were analyzed through bioinformatics. Five typical CSPs were identified in the P. fluorescens PF08 genome (PfCSPs). All five PfCSPs are small hydrophilic acidic proteins with a molecular mass of ca. 7.4 kDa. They are located in the cytoplasm and are nonsecretory and nontransmembrane proteins. Multiple sequence alignment analysis indicated that the CSPs are highly conserved between species, especially in DNA-binding sites and RNA-binding motifs that can bind to single-stranded DNA and RNA. The five PfCSPs clustered with CspD from Escherichia coli and Salmonella Typhimurium, which suggests a close homology and high functional similarity among the five PfCSPs and CspD. The secondary and tertiary structures of the PfCSPs are in accordance with the characteristics of the CSP family, and ligand binding sites with higher likelihood were found in PfCSPs. The five PfCSPs were predicted to interact with some of the same proteins that are involved in virulence, stress responses (including to low temperature), cell growth, ribosome assembly, and RNA degradation. The results provide further elucidation of the function of CSPs in adaptation to low temperatures by P. fluorescens.

HIGHLIGHTS

Skin Microbiota of the Captive Giant Panda (Ailuropoda Melanoleuca) and the Distribution of Opportunistic Skin Disease-Associated Bacteria in Different Seasons

The giant panda is one of the rarest animals in the world. Skin diseases seriously endanger the health of giant panda and are considered the second major cause of its morbidity. Skin microbiota is a complex ecosystem, and the community structure and the pathogenic potential of bacteria on giant panda skin remain largely unclear. In order to understand the skin bacterial flora of captive giant pandas, the microbiota in giant panda skin samples collected during different seasons was profiled via 16S rRNA gene sequencing. In total, 522 genera from 53 bacterial phyla were detected, with Proteobacteria (40.5%), Actinobacteria (23.1%), Firmicutes (21.1%), Bacteroidetes (9.5%), Cyanobacteria (2.1%), and Thermi (1.2%) as the predominant phyla and Streptococcus (13.9%), Acinetobacter (9.2%), Staphylococcus (2.9%), Pseudomonas (5.9%), Dermacoccus (4.8%), Brachybacterium (2.9%), Escherichia (2.7%), Chryseobacterium (2.1%), Arthrobacter (1.6%), Kocuria (1.5%), Psychrobacter (1.2%), Deinococcus (1.1%), and Flavobacterium (1.1%) as the predominant genera. The results indicated that the diversity was lower in winter than in other seasons and higher in autumn than in other seasons, and the abundance in spring was significantly higher than that in other seasons. Several skin disease-associated bacteria were detected as opportunists in the skin microbiota of healthy giant pandas. In this study, the results indicated that the high diversity and abundance of the skin bacteria may have enhanced the occurrence of skin disease in autumn and spring and that skin disease-associated bacteria are the normal components of the skin microbiota.

The burden of Arcanobacterium haemolyticum pharyngitis: A systematic review and management algorithm

INTRODUCTION

Arcanobacterium haemolyticum causes pharyngotonsillitis in children and young adults. It is rarely isolated in pharyngeal swabs as testing for it is not routine. Data on complications, management, and antibiotic susceptibility testing is limited. We sought to review the available literature on the presentation and management of A. haemolyticum pharyngotonsillitis in this age group.

METHODS

A systematic review of eligible studies reporting pharyngotonsillitis and related complications in children and young adults caused by A. haemolyticum was conducted. Literature from case reports, case series, and available cohorts was compiled. Data were analyzed using descriptive statistics.

RESULTS

The initial database search yielded 63 articles, after applying exclusion criteria 17 studies were included. 191 patients were identified with a median age of 16.5 years. The most common presentation was throat pain reported in 93.7% of patients. Tonsillar exudates, fever at presentation and rash were present in more than half of the reviewed cases. The diagnosis was established by a positive culture on a pharyngeal swab in 98.8% of swabs collected. Complications described included peritonsillar abscesses, Lemierre's syndrome, pneumonia, and sepsis. Penicillin was the first line antibiotic in 81% of patients followed by macrolides in 19 patients (18%).

CONCLUSIONS

A. haemolyticum occurs in children and young adults and may result in complications. Our review supports its susceptibility to penicillin. We suggest a diagnostic and management algorithm to guide clinicians in targeted testing and aid with decision making regarding timely and appropriate antibiotic therapy, in an effort to reduce the burden of its complications.

The Relevance of IL-1-Signaling in the Protection against Gram-Positive Bacteria

Previous studies performed using a model of group B streptococcus (GBS)-induced peritoneal inflammation indicate that the interleukin-1 receptor (IL-1R) family plays an important role in the innate host defense against this encapsulated Gram-positive bacteria. Since the role of IL-1-dependent signaling in peritoneal infections induced by other Gram-positive bacteria is unknown, in the present study we sought to investigate the contribution of IL-1R signaling in host defenses against Streptococcus pyogenes (group A streptococcus or GAS) or Staphylococcus aureus, two frequent and global human Gram-positive extracellular pathogens. We analyzed here the outcome of GAS or S. aureus infection in IL-1R-deficient mice. After inoculated intraperitoneal (i.p.) inoculation with group A Streptococcus or S. aureus, all the wild-type (WT) control mice survived the challenge, while, respectively, 63% or 50% of IL-1-defective mice died. Lethality was due to the ability of both bacterial species to replicate and disseminate to the target organs of IL-1R-deficient mice. Moreover, the experimental results indicate that IL-1 signaling promotes the production of leukocyte attractant chemokines CXCL-1 and CXCL-2 and recruitment of neutrophils to bacterial infection sites. Accordingly, the reduced neutrophil recruitment in IL-1R-deficient mice was linked with decreased production of neutrophil chemokines. Collectively, our findings indicate that IL-1 signaling, as previously showed in host defense against GBS, plays a fundamental role also in controlling the progression and outcome of GAS or S. aureus disease.

Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage

Streptococcus pyogenes is an important human pathogen worldwide. The identification of natural antibacterial phytochemicals has renewed interest due to the current scarcity of antibiotic development. Carvacrol is a monoterpenoid found in herbs. We evaluated carvacrol alone and combined with selected antibiotics against four strains of S. pyogenes in vitro. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of carvacrol against S. pyogenes were 125 µg/mL (0.53 mM) and 250 µg/mL (1.05 mM), respectively. Kill curve results showed that carvacrol exhibits instantaneous bactericidal activity against S. pyogenes. We also demonstrated the potential mechanism of action of carvacrol through compromising the cell membrane integrity. Carvacrol induced membrane integrity changes leading to leakage of cytoplasmic content such as lactate dehydrogenase enzymes and nucleic acids. We further confirmed dose-dependent rupturing of cells and cell deaths using transmission electron microscopy. The chequerboard assay results showed that carvacrol possesses an additive-synergistic effect with clindamycin or penicillin. Carvacrol alone, combined with clindamycin or penicillin, can be used as a safe and efficacious natural health product for managing streptococcal pharyngitis.

Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity

Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatranscriptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, biological traits such as coral life history strategy correlated with patterns of viral diversity. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect protists and algal cells, respectively. Further, Myoviridae and Siphoviridae presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, whereas Hepadnaviridae and Retroviridae might infect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common among the viral sequences, corroborating a contribution of viruses to the holobiont’s genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns.

The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression

Gene transfer and homologous recombination in Streptococcus pyogenes has the potential to trigger the emergence of pandemic lineages, as exemplified by lineages of emm1 and emm89 that emerged in the 1980s and 2000s, respectively. Although near-identical replacement gene transfer events in the nga (NADase) and slo (streptolysin O) loci conferring high expression of these toxins underpinned the success of these lineages, extension to other emm genotype lineages is unreported. The emergent emm89 lineage was characterized by five regions of homologous recombination additional to nga-slo, including complete loss of the hyaluronic acid capsule synthesis locus hasABC, a genetic trait replicated in two other leading emm types and recapitulated by other emm types by inactivating mutations. We hypothesized that other leading genotypes may have undergone similar recombination events. We analyzed a longitudinal data set of genomes from 344 clinical invasive disease isolates representative of locations across England, dating from 2001 to 2011, and an international collection of S. pyogenes genomes representing 54 different genotypes and found frequent evidence of recombination events at the nga-slo locus predicted to confer higher toxin genotype. We identified multiple associations between recombination at this locus and inactivating mutations within hasAB, suggesting convergent evolutionary pathways in successful genotypes. This included common genotypes emm28 and emm87. The combination of no or low capsule and high expression of nga and slo may underpin the success of many emergent S. pyogenes lineages of different genotypes, triggering new pandemics, and could change the way S. pyogenes causes disease.IMPORTANCEStreptococcus pyogenes is a genetically diverse pathogen, with over 200 different genotypes defined by emm typing, but only a minority of these genotypes are responsible for the majority of human infection in high-income countries. Two prevalent genotypes associated with disease rose to international dominance following recombination of a toxin locus that conferred increased expression. Here, we found that recombination of this locus and promoter has occurred in other diverse genotypes, events that may allow these genotypes to expand in the population. We identified an association between the loss of hyaluronic acid capsule synthesis and high toxin expression, which we propose may be associated with an adaptive advantage. As S. pyogenes pathogenesis depends both on capsule and toxin production, new variants with altered expression may result in abrupt changes in the molecular epidemiology of this pathogen in the human population over time.

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies.

Scarlet Fever Epidemic in China Caused by Streptococcus pyogenes Serotype M12: Epidemiologic and Molecular Analysis

From 2011, Hong Kong and mainland China have witnessed a sharp increase in reported cases, with subsequent reports of epidemic scarlet fever in North Asia and the United Kingdom. Here we examine epidemiological data and investigate the genomic context of the predominantly serotype M12 Streptococcus pyogenes scarlet fever isolates from mainland China. Incident case data was obtained from the Chinese Nationwide Notifiable Infectious Diseases Reporting Information System. The relative risk of scarlet fever in recent outbreak years 2011–2016 was calculated using the median age-standardised incidence rate, compared to years 2003–2010 prior this outbreak. Whole genome sequencing was performed on 32 emm12 scarlet fever isolates and 13 emm12 non-scarlet fever isolates collected from different geographic regions of China, and compared with 203 published emm12 S. pyogenes genomes predominantly from scarlet fever outbreaks in Hong Kong (n = 134) and the United Kingdom (n = 63). We found during the outbreak period (2011–2016), the median age-standardised incidence in China was 4.14/100,000 (95% confidence interval (CI) 4.11-4.18), 2.62-fold higher (95% CI 2.57-2.66) than that of 1.58/100,000 (95% CI 1.56-1.61) during the baseline period prior to the outbreak (2003 − 2010). Highest incidence was reported for children 5 years of age (80.5/100,000). Streptococcal toxin encoding prophage φHKU.vir and φHKU.ssa in addition to the macrolide and tetracycline resistant ICE-emm12 and ICE-HKU397 elements were found amongst mainland China multi-clonal emm12 isolates suggesting a role in selection and expansion of scarlet fever lineages in China. Global dissemination of toxin encoded prophage has played a role in the expansion of scarlet fever emm12 clones. These findings emphasize the role of comprehensive surveillance approaches for monitoring of epidemic human disease.

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The study used all epidemiological data from 1950 to 2016, and describe increased incidence levels for the current outbreak.

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Using global emm12 scarlet fever isolate genome sequences, the multiclonal nature of the outbreak was confirmed.

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Global surveillance of GAS toxin and drug resistance mobile genes in the scarlet fever outbreak is necessary.

Our study provides a detailed report of scarlet fever epidemiology and genomic analysis for mainland China since the 2011 outbreak began. We also provide a comprehensive comparison of the genomic relationship of scarlet fever outbreak emm12 isolates from China, Hong Kong and the United Kingdom, countries experiencing an unparalleled re-emergence of scarlet fever. Our observations implicate an important role for GAS toxin and drug resistance related mobile genes in the outbreak and reveal different evolutionary patterns, and identify common themes relating to the acquisition of toxin carrying prophage elements. This work emphasizes the importance of comprehensive nationwide surveillance to track scarlet fever, GAS emm types, exotoxin-encoding prophage and antibiotic resistance genes in a global context.