emm Typing of group A streptococcus clinical isolates: identification of dominant types for throat and skin isolates

Epidemiological shifts in and impact of COVID-19 on streptococcal toxic shock syndrome in Japan: A genotypic analysis of group A Streptococcus isolates

OBJECTIVES

Streptococcal toxic shock syndrome (STSS) is caused by group A Streptococcus (GAS; Streptococcus pyogenes) strains. In Japan, the number of STSS cases has decreased; however, the underlying reason remains unclear. Moreover, information on distribution and prevalence of specific emm types in STSS cases is scarce. Hence, we investigated the reason for the decreased number of STSS cases in Japan.

METHODS

We genotyped emm of 526 GAS isolates obtained from 526 patients with STSS between 2019 and 2022. The distributions of emm types in each year were compared.

RESULTS

The emm1 type was predominant, with the highest proportion in 2019, which decreased after 2020 following the onset of the coronavirus disease 2019 (COVID-19) pandemic. Strains isolated during the pandemic correlated with strains associated with skin infection, whereas those isolated during the prepandemic period correlated with strains associated with both throat and skin infections. The decrease in the annual number of STSS cases during the COVID-19 pandemic could be due to a decreased proportion of strains associated with pharyngeal infections.

CONCLUSIONS

Potential associations between pandemic and STSS numbers with respect to public health measures, such as wearing masks and changes in healthcare-seeking behavior, may have affected the number of GAS-induced infections.

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.

Decoding the molecular epidemiology of group A streptococcus - an Indian perspective

PURPOSE

Unlike western countries the knowledge of group A streptococcus (GAS) epidemiology in India remains patchy and incomplete. Typing is crucial for surveillance as well as in predicting the efficacy of multivalent M protein vaccine. The present study aimed to explore the emm types of 206 invasive and non-invasive GAS isolates from South India as well as reviewing all the published literature on GAS molecular epidemiology from India thereby generating a pan-Indian data to predict the conjectural coverage of the 30-valent M-protein vaccine in this population.

METHODOLOGY

emm typing and superantigen (SAg) profiling of GAS along with reviewing literatures on GAS molecular epidemiology from India.

RESULTS

This study revealed a high diversity of emm types with emm 63, 82, 183, 85, 92, 169, 42, 44, 106, 74, 12 being frequently encountered, belonging to twenty emm clusters. The pan-Indian data on prevalent emm types further supports our study findings with 135 emm different types. Six clusters dominated accounting for 80 % of the GAS isolates: E3(26 %), E6(20 %), E2(11 %), E4(10 %), D4(7 %), E1(6 %). No significant association was noted between emm types and the nature of infection (P≥0.05) while a few SAg profiles were significantly associated with certain emm types. Pan Indian data revealed that only 16 % of the emm types encountered were included in proposed 30-valent M protein based vaccine.

CONCLUSION

The coverage among the South Indian GAS isolates was 28.2 % which increased to only 46.6 % with the cross-opsonic effect, thus highlighting the importance of developing a specific multivalent vaccine including the prevalent emm types in India or considering the use of conserved C-repeat vaccines and non-M protein based vaccines.

DNA-based culture-independent analysis detects the presence of group a streptococcus in throat samples from healthy adults in Japan

Background

Group A Streptococcus (GAS; Streptococcus pyogenes) causes a range of mild to severe infections in humans. It can also colonize healthy persons asymptomatically. Therefore, it is important to study GAS carriage in healthy populations, as carriage of it might lead to subsequent disease manifestation, clonal spread in the community, and/or diversification of the organism. Throat swab culture is the gold standard method for GAS detection. Advanced culture-independent methods provide rapid and efficient detection of microorganisms directly from clinical samples. We investigated the presence of GAS in throat swab samples from healthy adults in Japan using culture-dependent and culture-independent methods.

Results

Two throat swab samples were collected from 148 healthy volunteers. One was cultured on selective medium, while total DNA extracted from the other was polymerase chain reaction (PCR) amplified with two GAS-specific primer pairs: one was a newly designed 16S rRNA-specific primer pair, the other a previously described V-Na⁺-ATPase primer pair. Although only 5 (3.4 %) of the 148 samples were GAS-positive by the culture-dependent method, 146 (98.6 %) were positive for the presence of GAS DNA by the culture-independent method. To obtain serotype information by emm typing, we performed nested PCR using newly designed emm primers. We detected the four different emm types in 25 (16.9 %) samples, and these differed from the common emm types associated with GAS associated diseases in Japan. The different emm types detected in the healthy volunteers indicate that the presence of unique emm types might be associated with GAS carriage.

Conclusions

Our results suggest that culture-independent methods should be considered for profiling GAS in the healthy hosts, with a view to obtaining better understanding of these organisms. The GAS-specific primers (16S rRNA and V-Na⁺-ATPase) used in this study can be used to estimate the maximum potential GAS carriage in people.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0858-5) contains supplementary material, which is available to authorized users.

Outbreak of Streptococcus pyogenes emm type 58 in a high dependency unit of a level-1 trauma center of India

Background and Aims:

Group A Streptococcus (GAS) can cause illnesses ranging from self-limited to severe, life-threatening, invasive infections. The objective of the following study was to investigate a suspected Streptococcus pyogenes outbreak in a high dependency unit (HDU) of our trauma center.

Materials and Methods:

All the isolates of beta hemolytic Streptococci were identified by standard microbiological methods, Vitek 2 system and latex agglutination tests. Antimicrobial susceptibility testing was performed as recommended by Clinical Laboratory Standards Institute. Exotoxin genes, including speA, speB, speC, speF, smeZ, ssa, speG, speH, speJ, speL, speM and speI were detected by polymerase chain reaction (PCR). The emm types of isolates of S. pyogenes were determined by sequencing the variable 5’ end of emm gene after amplification by PCR.

Results:

In a 28 bedded poly-trauma ward with a four bedded HDU three out of four patients developed S. pyogenes emm type 58 infection. The strain was macrolide and tetracycline resistant and produced the Streptococcal pyrogenic exotoxins speB, speC, speG, speF and smeZ. Surveillance sampling was done for investigation from patients, health-care workers and environmental samples.

Conclusion:

An outbreak of GAS infections was established caused by the uncommonly reported emm type 58. The outbreak was controlled by prompt treatment, intensive surveillance, feedback and training.

Study of T serotypes and Emm genotypes of Streptococcus pyogenes in children with pharyngitis and tonsillitis

Streptococcus pyogenes, or group A Streptococcus (GAS), causes superficial infections of the upper respiratory tract that manifest as diseases such as pharyngitis and tonsillitis. T serotypes, emm genotypes, and the antimicrobial susceptibility of GAS isolated from the pharynges of patients with pharyngitis and tonsillitis were studied. The two most common T serotypes were T12 (10/25: 40%) and T1 (7/25: 28%), and the two most common emm genotypes were emm12 (12/27: 44%) and emm1 (7/27: 26%). Good correlation was observed between these T serotypes and emm genotypes.

Factors associated with Group A Streptococcus emm type diversification in a large urban setting in Brazil: a cross-sectional study

BACKGROUND

Group A Streptococcus (GAS) strain diversity varies across different regions of the world, according to low versus high-income countries. These differences may be related to geographic, environmental, socioeconomic, or host-related factors. However, local factors may also affect strain diversity. We compared the emm types of GAS isolates from children with and without sore throat in one large urban setting in Brazil.

METHODS

Children 3-15 years of age were consecutively recruited from slum and non-slum pediatric outpatient clinics between April-October, 2008. Throat cultures were performed and data intake forms were completed. GAS isolates were typed by emm sequencing.

RESULTS

From 2194 children, 254 (12%) GAS isolates were obtained. Of 238 GAS isolates that were emm-typed, 61 unique emm types were identified. Simpson's diversity index of the emm types was higher among isolates from slum children [97% (96%-98%)] than those of non-slum children [92% (89%-96%)]. Two emm types (66.0, 12.0) were more frequently isolated from children with sore throat (p < 0.05), and one emm type (27G.0) demonstrated a protective effect.

CONCLUSIONS

The emm type diversity from children attending slum clinics resembled the emm diversity of low income countries rather than that of children attending a non-slum clinic in the same city. Local factors, such as crowding, may enhance the frequency of GAS transmission and horizontal gene transfers that contribute to increased strain diversity in the slums. GAS vaccine coverage and control of GAS infections will need to take these local factors and strain differences into consideration.

Group A streptococcal genotypes from throat and skin isolates in the United Arab Emirates

Background

The bacterium Streptococcus pyogenes causes a variety of human diseases that range from relatively mild skin infections to severe invasive diseases, such as acute rheumatic fever, glomerulonephritis, puerperal sepsis, necrotizing fasciitis, meningitis, and streptococcal toxic shock syndrome. Accurate identification and typing of group A hemolytic streptococci (GAS) is essential for epidemiological and pathogenetic studies of streptococcal diseases. For this reason, The genetic diversity of group A streptococcal (GAS) isolates from subjects in the United Arab Emirates with streptococcal disease was studied using emm gene sequence analysis. The emm typing system which is based on sequence analysis of PCR products of the N-terminal hypervariable region of the M protein gene, concurs with M serotyping almost 1:1.

Findings

A total of 38 GAS isolates were analyzed, including 35 isolates from throat and 3 from skin. Among the 38 isolates, a total of 25 different emm/st types were detected: 20 isolates (53%) belonged to 16 validated standard reference emm types and 18 isolates (47%) belonged to 9 recognized sequence types.

Conclusions

This is the first emm typing study in the United Arab Emirates to demonstrate the heterogeneity of the GAS population.

Distribution of fibronectin-binding protein genes (prtF1 and prtF2) and streptococcal pyrogenic exotoxin genes (spe) among Streptococcus pyogenes in Japan

Two hundred and seventy-two strains of Streptococcus pyogenes isolated from patients with invasive and noninvasive infections in Japan were evaluated for the prevalence of fibronectin-binding protein genes (prtF1 and prtF2). The possible associations of the genes with streptococcal pyrogenic exotoxin genes, macrolide resistance genes, and emm types were also evaluated. Overall, about 50% of S. pyogenes isolates carried fibronectin-binding protein genes. The prevalence of the prtF1 gene was significantly higher among isolates from noninvasive infections (71.4%) than among isolates from invasive infections (30.8%; P = 0.0037). Strains possessing both the prtF1 and prtF2 genes were more likely to be isolates from noninvasive infections than isolates from invasive infections (50.6% vs 15.4%; P = 0.019). S. pyogenes isolates with streptococcus pyrogenic exotoxin genes (speA and speZ) were more common among isolates without fibronectin-binding protein genes. The speC gene was more frequently identified among isolates with fibronectin-binding protein genes (P = 0.05). Strains belonging to emm75 or emm12 types more frequently harbored macrolide resistance genes than other emm types (P = 0.0094 and P = 0.043, respectively). Strains carrying more than one repeat at the RD2 region of the prtF1 gene and the FBRD region of the prtF2 gene were more prevalent among strains with macrolide resistance genes than among strains negative for macrolide resistance genes. These genes (i.e., the prtF1, prtF2, and spe genes) may enable host-bacteria interaction, and internalization in the host cell, but may not enable infection complications such as invasive diseases.

Genetic analysis of group A streptococcus isolates recovered during acute glomerulonephritis outbreaks in Guizhou Province of China

In this study, 68 group A streptococcus (GAS) isolates associated with two outbreaks of acute glomerulonephritis (AGN) in China were analyzed by emm typing. A total of 11 different emm types were identified. Analysis of emm type distribution suggested that AGN outbreaks in two counties were caused by emm60.1- and emm63.0-type GAS. These two types were further characterized by pulsed-field gel electrophoresis, multilocus sequence typing, sof sequence typing, and PCR-based identification of streptococcal pyrogenic exotoxin A, B, and C (speA, speB, and speC) genes. In antimicrobial susceptibility tests, all outbreak strains were resistant to erythromycin and tetracycline, and the rates of resistance of nonoutbreak strains to the two antibiotics were 63.6% and 90.9%. This study is also the first to report a nephritogenic M63 GAS strain.

Distribution of emm types and subtypes among noninvasive group A, C and G streptococcal isolates in western Norway

Characterization of the reservoir of beta-hemolytic streptococci in a community may shed light on the pathogenesis of severe infections caused by these bacteria. We used emm sequence typing to characterize group A streptococci (GAS), group C streptococci (GCS) and group G streptococci (GGS) in community isolates associated with noninvasive disease in western Norway. A total of 165 isolates during a 13-month period were examined. Skin and throat isolates accounted for 123 and 16, respectively, and the remaining 26 isolates were from other non-sterile sites. We identified 18 previously validated emm types and one novel subtype, emm11.7, among the 101 GAS isolates. The two predominant types, emm28 and 12, were found in 40.6% of the GAS isolates. Compared to other recent studies of noninvasive GAS infections from elsewhere in the world, we found a higher frequency of emm82 (5.9%) and emm87 (12.9%) and a lower frequency of emm1 (4.0%) and emm3 (4.0%). We found a different distribution of GAS emm types compared to a previous study from western Norway. Among the 64 isolates of GCS and GGS, 15 previously described emm types and four novel subtypes, stC1400.5, stCK401.3, stG6.3 and stG652.3, were found, stG6, stG643 and stG485 were the most prevalent types and accounted for 59.4% of the GCS and GGS isolates. The high proportion of skin isolates in the present study may indicate the existence of GAS, GCS and GGS strains with predominantly skin and soft tissue tropism in our community.

Comparative analysis of emm type pattern of Group A Streptococcus throat and skin isolates from India and their association with closely related SIC, a streptococcal virulence factor

Background

Group A streptococcus (GAS) causes a wide variety of life threatening diseases in humans and the incidence of such infections is high in developing countries like India. Although distribution of emm types of GAS in India has been described, there is a lack of data describing either the comparative distribution of emm types in throat versus skin isolates, or the distribution of certain virulence factors amongst these isolates. Therefore in the present study we have monitored the emm type pattern of Group A streptococcus throat and skin isolates from India. Additionally, the association of these isolates with closely related sic (crs), a multifunctional compliment binding virulence factor, was also explored.

Results

Of the 94 (46 throat and 48 skin) isolates analyzed, 37 emm types were identified. The most frequently observed emm types were emm49 (8.5%) and emm112 (7.5%) followed by 6.5% each of emm1-2, emm75, emm77, and emm81. Out of 37 emm types, 27 have been previously reported and rest were isolated for the first time in the Indian Community. The predominant emm types of throat (emm49 and emm75) samples were different from those of skin (emm44, emm81 and emm112) samples. After screening all the 94 isolates, the crs gene was found in six emm1-2 (crs1-2) isolates, which was confirmed by DNA sequencing and expression analysis. Despite the polymorphic nature of crs, no intravariation was observed within crs1-2. However, insertions and deletions of highly variable sizes were noticed in comparison to CRS isolated from other emm types (emm1.0, emm57). CRS1-2 showed maximum homology with CRS57, but the genomic location of crs1-2 was found to be the same as that of sic1.0. Further, among crs positive isolates, speA was only present in skin samples thus suggesting possible role of speA in tissue tropism.

Conclusion

Despite the diversity in emm type pattern of throat and skin isolates, no significant association between emm type and source of isolation was observed. The finding that the crs gene is highly conserved even in two different variants of emm1-2 GAS (speA +ve and -ve) suggests a single allele of crs may be prevalent in the highly diverse throat and skin isolates of GAS in India.

Genetic features of clinical isolates of Streptococcus dysgalactiae subsp. equisimilis possessing Lancefield's group A antigen

Thirteen Streptococcus dysgalactiae subsp. equisimilis isolates possessing Lancefield's group A antigen recovered from people in Japan during 2000 to 2004 were genotyped. The results indicate that a conserved clone has persisted and spread within Japan, and two different emm types were observed within members of this clone.

The dynamic nature of group A streptococcal epidemiology in tropical communities with high rates of rheumatic heart disease

Prospective surveillance was conducted in three remote Aboriginal communities with high rates of rheumatic heart disease in order to investigate the epidemiology of group A beta-haemolytic streptococci (GAS). At each household visit, participants were asked about sore throat. Swabs were taken from all throats and any skin sores. GAS isolates were emm sequence and pattern-typed using standard laboratory methods. There were 531 household visits; 43 different emm types and subtypes (emmST) were recovered. Four epidemiological patterns were observed. Multiple emmST were present in the population at any one time and household acquisition rates were high. Household acquisition was most commonly via 5- to 9-year-olds. Following acquisition, there was a 1 in 5 chance of secondary detection in the household. Throat detection of emmST was brief, usually <2 months. The epidemiology of GAS in these remote Aboriginal communities is a highly dynamic process characterized by emmST diversity and turnover.

Molecular characterization of clinical isolates of M non-typable group A streptococci from invasive disease cases

Currently there are 93 validated M serotypes of Streptococcus pyogenes, Lancefield group A streptococcus (GAS), and >130 emm genotypes. A marked increase in the number of non-typable GAS isolates (2 % in 2000, 4 % in 2001 and 9 % in 2002) from invasive disease cases referred to the authors' reference laboratory was noted during 2000–2002. A total of 217 (92 %) were from blood cultures, 14 (6 %) from deep abscesses and five (2 %) from aspirates. The clinical manifestations included bacteraemia, septicaemia, cellulitis, meningitis, necrotizing fasciitis and toxic-shock syndrome. In order to establish whether this increase was due to the emergence of novel types or the unavailability of M-typing sera, these isolates were subjected to emm sequencing. A total of 144 isolates (61 %) belonged to M types for which sera were no longer available; 112 (48 %) belonged to higher M types, including emm83.1 (9 %), emm94 (8 %) emm87 (6 %) and emm89 (6 %); and 32 (13 %) belonged to lower M types that were not commonly isolated in the UK, and included M25, M43, M49, M64, M73 and M74. Sixty-six (28 %) of the isolates belonged to newly designated emm types. Other isolates belonged to the novel emm types st2147, STNS1033 and st854, recently registered in the Centers for Disease Control (CDC) database by other laboratories. One novel emm type, st2161, was isolated from an injecting drug user. There were differences in the type distribution of these isolates according to geographic location. However, 90 % of emm93, one of seven predominant emm types identified amongst the collection of M non-typable (MNT) isolates, were isolated from the London region.

High diversity of group A streptococcal emm types among healthy schoolchildren in Ethiopia

BACKGROUND

Although the prevalence of rheumatic heart disease in Ethiopia is one of the highest in the world, the epidemiology of group A streptococci (GAS) in this country is little known. GAS typing is a hallmark of both the epidemiology and understanding of diseases caused by these organisms. We have therefore conducted this study to investigate the emm (M-protein gene) type distribution of GAS carriers among Ethiopian schoolchildren.

METHODS

In the present study, we performed emm typing of 82 GAS isolates collected from the throats of healthy schoolchildren (6-14 years of age) residing in 3 different urban sites in Ethiopia: Addis Ababa, Gondar, and Dire Dawa.

RESULTS

We report high diversity of GAS isolates recovered from healthy schoolchildren. Eighty-two isolates represented 43 different sequence types. Thirteen newly described subtypes were detected in this study. Of the emm types prevalent in the study communities, 46% were not included in the 26-valent GAS vaccine.

CONCLUSIONS

The high diversity of emm types encountered within 3 months of collection suggest that production of a vaccine candidate based on the M-protein amino termini appears to be impractical for this population. We suggest that investigations of other vaccine candidates, including the C5a peptidase, GAS carbohydrate, and fibronectin-binding proteins, as well as conserved M-protein region vaccines, should be intensified to address the needs of this population.

M protein gene (emm type) analysis of group A beta-hemolytic streptococci from Ethiopia reveals unique patterns

The genetic diversity of group A streptococcal (GAS) isolates obtained in 1990 from Ethiopian children with various streptococcal diseases was studied by using emm gene sequence analysis. A total of 217 GAS isolates were included: 155 and 62 isolates from throat and skin, respectively. A total of 78 different emm/st types were detected among the 217 isolates. Of these, 166 (76.5%) belonged to 52 validated reference emm types, 26 (11.9%) belonged to 16 already recognized sequence types (st types) and 25 (11.5%) belonged to 10 undocumented new sequence types. Resistance to tetracycline (148 of 217) was not correlated to emm type. Isolation rate of the classical rheumatogenic and nephritogenic strains was low from cases of acute rheumatic fever (ARF) and acute glomerulonephritis (AGN), respectively. Instead, the recently discovered st types were overrepresented among isolates from patients with ARF (3 of 7) and AGN (9 of 16) (P < 0.01) compared to isolates from subjects with tonsillitis and from healthy carriers (10 of 57 and 16 of 90, respectively). In contrast to rheumatogenic strains from the temperate regions, more than half of the isolates from ARF (four of seven) carried the genetic marker for skin preference, emm pattern D, although most of them (six of seven) were isolated from throat. Of 57 tonsillitis-associated isolates, 16 (28%) belonged to emm pattern D compared to <1% in temperate regions. As in other reports emm patterns A to C were strongly associated with throat, whereas emm pattern D did not correlate to skin. This first large-scale emm typing report from Africa has demonstrated a heterogeneous GAS population and contrasting nature of GAS epidemiology in the region.

Genetic diversity among type emm28 group A Streptococcus strains causing invasive infections and pharyngitis

Genome sequencing of group A Streptococcus (GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the emm gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the emm28 gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the emm28 gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (mefA, ermB, and ermTR) was analyzed by PCR, and less than 2% of the strains were positive.

Survey of emm gene sequences from pharyngeal Streptococcus pyogenes isolates collected in Spain and their relationship with erythromycin susceptibility

We conducted a nationwide survey of the variable 5' emm (M protein gene) sequences from 614 pharyngeal Streptococcus pyogenes isolates susceptible (299 isolates) and resistant (315 isolates) to erythromycin that were isolated in Spain from 1996 to 1999. Almost 98% of these isolates had emm sequences in agreement with previously recorded M antigen association. We only identified a new 5' emm sequence in 17 isolates. Nine different emm types accounted for 85% of the S. pyogenes isolates susceptible to erythromycin. By contrast, only 3 emm types accounted for 70% of the erythromycin-resistant isolates. Further characterization of these isolates by ribotyping and pulsed-field gel electrophoresis indicated that high frequency of erythromycin resistance in Spain is due to few clones.