Variations in the distribution of genes encoding virulence and extracellular proteins in group A streptococcus are largely restricted to 11 genomic loci

Case Report: Septic arthritis in children caused by Streptococcus pyogenes-rational use of antibiotics

To investigate the clinical characteristics and treatment of septic arthritis caused by Streptococcus pyogenes(S. pyogenes) in children, we retrospectively analyzed the clinical data, laboratory results, treatments and outcomes of three pediatric cases of septic arthritis caused by S. pyogenes occurring from 2016-2018. The three cases of septic arthritis included 1 boy and 2 girls, aged from 2-7 years. Two patients experienced fever, and in all three cases, the affected joints showed redness, swelling, an increased local skin temperature, tenderness and restricted limb movement. At the first visit, all three cases showed a significantly increased white blood cell count [(27.68-32.02)×10⁹/mL] and a significantly increased erythrocyte sedimentation rate (113-134 mm/h). The C-reactive protein level was significantly increased in two cases (67 mg/L, 147.7 mg/L) and normal in one case. The procalcitonin level was normal in 1 case, elevated in 1 case, and undetected in 1 case. S. pyogenes isolated from cases 1 and 2 were emm1/ST28 and from case 3 was emm12/ST36. All patients were treated by abscess incision and drainage, and S. pyogenes was cultured in the abscess puncture fluid. All patients were treated with intravenous antibiotics after admission, and all patients were cured and discharged. The patients were followed up for 2 months, and their condition was improved and stable. No sequelae such as heart and kidney damage were detected. In conclusion, for children with septic arthritis, early diagnosis and timely treatment with incision and drainage followed by culture of the abscess puncture fluid are important. Once S. pyogenes infection is confirmed, β-lactam antibiotics provide effective treatment, avoiding use of broad-spectrum antibiotics.

In Silico Investigation for Evaluation of the Potential of the SclA Protein in Streptococcus pyogenes

Background:

Streptococcus pyogenes is an important pathogen that is associated with a range of infections in humans, and causes common and severe invasive diseases. Currently, antimicrobial therapy is the first choice for the treatment of S. pyogenes; however, the emergence of antimicrobial resistance and side effects of antibacterial drugs is increasing. Consequently, there is an increased demand for novel drug targets and vaccine design.

Objectives:

To develop an effective vaccine against Streptococcus pyogenes (group A streptococcus) , we described a novel collagen-like surface protein of S. pyogenes which is important virulence factors

Materials and Methods:

In this study, we focused on the SclA protein of S. pyogenes and characterized it using bioinformatic tools to introduce it as a candidate novel drug as a candidate for use in vaccine design. The secondary structure was determined and the 3D structure was modeled using SWISS-MODEL workspace. The immune epitope database analysis (IEDB) resource was used to predict regions of SclA that are likely to be recognized as epitopes.

Results:

The SclA protein is present on the cell surface of the cell and has interact with a common ligand by its hypervariable NH2-terminal regions. The IEDB showed that the maximum peptide length that is likely to be predicted as an epitope is of 6 amino acids, from amino acid 26 to 31, with a score of 4.791. This epitope can be considered for use in Antibody and drug design.

Conclusions:

Data from this study about SclA were not sufficient and further studies are needed; however, the information here suggests that SclA could be a candidate for further research on the design of drugs and vaccines against S. pyogenes infections.

Distribution of small native plasmids in Streptococcus pyogenes in India

Complete characterization of a Streptococcus pyogenes population from a defined geographic region comprises information on the plasmids that circulate in these bacteria. Therefore, we determined the distribution of small plasmids (<5kb) in a collection of 279 S. pyogenes isolates from India, where diversity of strains and incidence rates of S. pyogenes infections are high. The collection comprised 77 emm-types. For plasmid detection and discrimination, we developed PCRs for different plasmid replication initiation protein genes, the putative repressor gene copG and bacteriocin genes dysA and scnM57. Plasmid distribution was limited to 13 emm-types. Co-detection analysis using aforementioned PCRs revealed four distinct plasmid sub-types, two of which were previously unknown. Representative plasmids pA852 and pA996 of the two uncharacterized plasmid sub-types were sequenced. These two plasmids could be assigned to the pMV158 and the pC194/pUB110 family of rolling-circle plasmids, respectively. The majority of small plasmids found in India belonged to the two newly characterized sub-types, with pA852- and pA996-like plasmids amounting to 42% and 22% of all detected plasmids, respectively. None of the detected plasmids coded for a known antibiotic resistance gene. Instead, all of the four plasmid sub-types carried known or potential bacteriocin genes. These genes may have influence on the evolutionary success of certain S. pyogenes genotypes. Notably, pA852-like plasmids were found in all isolates of the most prevalent emm-type 11.0. Together, a priori fitness of this genotype and increased fitness due to the acquired plasmids may have rendered type emm11.0 successful and caused the prevalence of pA852-like plasmids in India.

Emergence of Streptococcus pyogenes emm102 causing toxic shock syndrome in Southern Taiwan during 2005-2012

BACKGROUND

Streptococcal toxic shock syndrome (STSS) is an uncommon but life-threatening disease caused by Streptococcus pyogenes.

METHODS

To understand the clinical and molecular characteristics of STSS, we analyzed clinical data and explored the emm types, superantigen genes, and pulsed-field gel electrophoresis of causative S. pyogenes isolates obtained between 2005 and 2012.

RESULTS

In total, 53 patients with STSS were included in this study. The median age of the patients was 57 years (range: 9-83 years), and 81.1% were male. The most prevalent underlying disease was diabetes mellitus (45.3%). Skin and soft-tissue infection accounted for 86.8% of STSS. The overall mortality rate was 32.1%. Underlying diseases had no statistical impact on mortality. A total of 19 different emm types were identified. The most prevalent emm type was emm102 (18.9%), followed by emm11 (17%), emm1 (11.3%), emm87 (9.4%), and emm89 (7.5%). There was no statistically significant association between emm type and a fatal outcome. Among the superantigen genes, speB was the most frequently detected one (92.5%), followed by smeZ (90.6%), speG (81.1%), speC (39.6%), and speF (39.6%). The majority of emm102 strains were found to have speB, speC, speG, and smeZ. The presence of speG was negatively associated with a fatal outcome (P = 0.045).

CONCLUSIONS

Our surveillance revealed the emergence of uncommon emm types, particularly emm102, causing STSS in southern Taiwan. Characterization of clinical, epidemiological, and molecular characteristics of STSS will improve our understanding of this life-threatening disease.

Streptococcal superantigens: categorization and clinical associations

Superantigens are key virulence factors in the immunopathogenesis of invasive disease caused by group A streptococcus. These protein exotoxins have also been associated with severe group C and group G streptococcal infections. A number of novel streptococcal superantigens have recently been described with some resulting confusion in their classification. In addition to clarifying the nomenclature of streptococcal superantigens and proposing guidelines for their categorization, this review summarizes the evidence supporting their involvement in various clinical diseases including acute rheumatic fever.

Changes in Streptococcus pyogenes causing invasive disease in Portugal: evidence for superantigen gene loss and acquisition

The emergence of highly virulent and successful Streptococcus pyogenes (group A streptococci - GAS) clones has been attributed to the exchange of virulence factors by lateral gene transfer mechanisms, which strongly contribute to genomic diversity. We characterized a collection of 191 GAS isolates recovered from normally sterile sites in Portugal during 2006-2009 and compared them to invasive isolates obtained during 2000-2005. Antimicrobial resistance rates did not change significantly between the two periods and were generally low. In 2006-2009, emm1, emm89, emm3, and emm6 represented 60% of the isolates. The chromosomally encoded superantigen (SAg) genes speG and smeZ were present in the majority (>90%) of the isolates, while speJ was found in only 45%. The phage encoded SAgs varied greatly in prevalence (2-53%). The distribution of emm types, pulsed-field gel electrophoresis profiling (PFGE) clusters, and SAg profiles changed significantly between the periods, although there were no statistically supported changes in the prevalence of individual types. While the macrolide susceptible clone emm1-T1-ST28 remained dominant (28%), there was a significant decrease in clonal diversity as indicated by both PFGE profiling and emm typing. This was accompanied by intra-clonal divergence of SAg profiles, which was statistically confirmed for isolates representing emm1, emm28, and emm44. This diversification was associated with the loss and acquisition of SAg genes, carried by phages and of chromosomal origin. These data suggest an ongoing genomic diversification of GAS invasive isolates in Portugal that may contribute to the persistence of clones with improved fitness or virulence.

Variability in the distribution of genes encoding virulence factors and putative extracellular proteins of Streptococcus pyogenes in India, a region with high streptococcal disease burden, and implication for development of a regional multisubunit vaccine

Streptococcus pyogenes causes a wide variety of human diseases and is a significant cause of morbidity and mortality. Attempts to develop a vaccine were hampered by the genetic diversity of S. pyogenes across different regions of the world. This study sought to identify streptococcal antigens suitable for a region-specific vaccine in India. We used a two-step approach, first performing epidemiological analysis to identify the conserved antigens among Indian isolates. The second step consisted of validating the identified antigens by serological analysis. The 201 streptococcal clinical isolates from India used in this study represented 69 different emm types, with emm12 being the most prevalent. Virulence profiling of the North and South Indian S. pyogenes isolates with a custom-designed streptococcal virulence microarray identified seven conserved putative vaccine candidates. Collagen-like surface protein (SCI), putative secreted 5'-nucleotidase (PSNT), and C5a peptidase were found in 100% of the isolates, while R28, a putative surface antigen (PSA), and a hypothetical protein (HYP) were found in 90% of the isolates. A fibronectin binding protein, SfbI, was present in only 78% of the isolates. In order to validate the identified potential vaccine candidates, 185 serum samples obtained from patients with different clinical manifestations were tested for antibodies. Irrespective of clinical manifestations, serum samples showed high antibody titers to all proteins except for SCI and R28. Thus, the data indicate that PSNT, C5a peptidase, PSA, HYP, and SfbI are promising candidates for a region-specific streptococcal vaccine for the different parts of India.

Superantigen gene complement of Streptococcus pyogenes--relationship with other typing methods and short-term stability

The profiling of the superantigen (SAg) encoding genes has been frequently used as a complementary typing method for group A streptococci (GAS), but a confusing gene nomenclature and a large diversity of primers used in screening has led to some conflicting results. The aim of this work was to develop a polymerase chain reaction (PCR) method capable of efficiently amplifying all the known allelic variants of these genes, and to evaluate the congruence of this methodology with other commonly used molecular typing methods. The presence of the 11 known SAg genes and two other exotoxin-encoding genes (speB and speF) was tested in a collection of 480 clinical GAS isolates, using two multiplex PCR reactions. The SAg gene profile was compared with other typing methods. Four naturally occurring deletions involving the genes speB, speF, and rgg were characterized, two of which were found among invasive isolates. The absence of the chromosomally encoded genes speG and smeZ was supported by Southern blot hybridization and associated with specific GAS lineages, while the presence of phage-encoded genes was more variable. Positive associations between SAg genes or between SAg profiles and emm types or pulsed-field gel electrophoresis (PFGE) clusters were observed. The results suggest that the SAg profile diversifies faster than other properties commonly used for molecular typing, such as emm type and multilocus sequence typing (MLST) sequence types (STs), and can be a useful complement in GAS molecular epidemiology. Still, the short-term stability of the SAg gene profile among prevalent genetic lineages may largely explain the observed associations between SAg genes.

Virulence gene pool detected in bovine group C Streptococcus dysgalactiae subsp. dysgalactiae isolates by use of a group A S. pyogenes virulence microarray

A custom-designed microarray containing 220 virulence genes of Streptococcus pyogenes (group A Streptococcus [GAS]) was used to test group C Streptococcus dysgalactiae subsp. dysgalactiae (GCS) field strains causing bovine mastitis and group C or group G Streptococcus dysgalactiae subsp. equisimilis (GCS/GGS) isolates from human infections, with the latter being used for comparative purposes, for the presence of virulence genes. All bovine and all human isolates carried a fraction of the 220 genes (23% and 39%, respectively). The virulence genes encoding streptolysin S, glyceraldehyde-3-phosphate dehydrogenase, the plasminogen-binding M-like protein PAM, and the collagen-like protein SclB were detected in the majority of both bovine and human isolates (94 to 100%). Virulence factors, usually carried by human beta-hemolytic streptococcal pathogens, such as streptokinase, laminin-binding protein, and the C5a peptidase precursor, were detected in all human isolates but not in bovine isolates. Additionally, GAS bacteriophage-associated virulence genes encoding superantigens, DNase, and/or streptodornase were detected in bovine isolates (72%) but not in the human isolates. Determinants located in non-bacteriophage-related mobile elements, such as the gene encoding R28, were detected in all bovine and human isolates. Several virulence genes, including genes of bacteriophage origin, were shown to be expressed by reverse transcriptase PCR (RT-PCR). Phylogenetic analysis of superantigen gene sequences revealed a high level (>98%) of identity among genes of bovine GCS, of the horse pathogen Streptococcus equi subsp. equi, and of the human pathogen GAS. Our findings indicate that alpha-hemolytic bovine GCS, an important mastitis pathogen and considered to be a nonhuman pathogen, carries important virulence factors responsible for virulence and pathogenesis in humans.

A novel integrative conjugative element mediates genetic transfer from group G Streptococcus to other {beta}-hemolytic Streptococci

Lateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including beta-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, from Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE from Streptococcus agalactiae (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider beta-hemolytic streptococcal population.

Genetic variation in group A streptococci

Group A streptococcus (GAS) is responsible for a range of human diseases that vary in their clinical manifestations and severity. While numerous virulence factors have been described, the way these factors interact to promote different streptococcal diseases is less clear. In order to identify multifactorial relationships between GAS and the human host, novel high-throughput techniques such as microarrays are necessary. We have performed comparative studies using custom-designed virulence arrays to enhance our understanding of the high degree of genotypic variation that occurs in streptococci. This study has pointed to mobile genetic elements as the major agents that promote variation. Our results show that multiple combinations of genes might bring about similar clinical pictures. This adds further complexity to the intricate relationship between pathogen and host.

Virulence profiling of Streptococcus dysgalactiae subspecies equisimilis isolated from infected humans reveals 2 distinct genetic lineages that do not segregate with their phenotypes or propensity to cause diseases

BACKGROUND

In spite of the emerging importance of Streptococcus dysgalactiae subspecies equisimilis (human group C streptococci [GCS] and group G streptococci [GGS]) in human health, its molecular makeup remains largely undefined. Apart from sharing a phylogenetic relationship with the human pathogen group A streptococci (GAS), GCS/GGS and GAS colonize the same ecological niche and exhibit considerable overlap in their disease profiles. Such similarities imply that the virulence factors associated with diseases may also be similar.

METHODS

In this study, we used a targeted microarray containing 216 GAS virulence genes to profile the virulence gene repertoires of 58 S. dysgalactiae subspecies equisimilis isolates recovered during human infections. We performed comparative analyses to investigate the relationship between GAS virulence genes in and the invasive potential of GCS/GGS.

RESULTS

Up to one-half of the GAS virulence genes represented in the microarray were identified in GCS/GGS. No statistical differences were observed between isolates harboring the group C versus group G carbohydrates; however, clustering algorithms revealed 2 genetically distinct clusters of S. dysgalactiae subspecies equisimilis isolates. No relationship was observed between the virulence profile of GCS/GGS and the propensity for disease or the tissue site of isolation.

CONCLUSIONS

This is, to our knowledge, the first comprehensive analysis of the virulence profile of S. dysgalactiae subspecies equisimilis, and it enables novel insights into the pathogen's genetic basis of disease propensity shared with GAS. Human group C and group G streptococci may not be considered to be separate species; in fact, they may constitute 2 distinct lineages. Additional incongruent relationships were observed between virulence profiles and GCS/GGS disease propensity.