Epidemiological study of erythromycin-resistant Streptococcus pyogenes from Korea and Japan by emm genotyping and multilocus sequence typing

A survey of antibiotic resistance patterns among Group A Streptococcus isolated from invasive and non-invasive infections in Cape Town, South Africa

Background

There is concern regarding the increasing resistance of Group A streptococcus (GAS) to routinely used antibiotics. GAS is a common cause of bacterial pharyngitis and more severe invasive infections such as septicaemia. Furthermore, GAS pharyngitis is the antecedent for serious conditions such as rheumatic fever and rheumatic heart disease. The study aimed to determine the antimicrobial susceptibility patterns of GAS cultured from patients with invasive and non-invasive infections from Cape Town, as part of the AFROStrep Registry.

Methods

Samples were provided by the AFROStrep Registry, a continental endeavour aiming to document Streptococcus pyogenes infection in Africa and create the first biorepository of its kind. Ninety-five GAS isolates (invasive, n = 40; non-invasive, n = 55) were evaluated for resistance to a panel of 20 antibiotics using the Sensititre® STP6F system with MICs interpreted by CLSI break points.

Results

Amongst all isolates, highest levels of resistance were observed with respect to tetracycline (8.33 %), followed by azithromycin (1.04 %) and erythromycin (1.04 %). No resistance to the remaining antibiotics was detected amongst all isolates. No differences with regard to MIC values were observed between isolates from invasive and non-invasive infections (p-value >0.05 for all antibiotics).

Conclusion

GAS remains susceptible to routine-antimicrobial agents used in our low-resourced setting. Eight percent of the GAS isolates were resistant to tetracycline, and we did not observe macrolide resistance as reported in high income countries. This is the first study to report on the antimicrobial patterns of GAS in South Africa. These results address a critical gap in the available data on GAS in Africa and specifically South Africa and, thus, aid in avoiding therapeutic failures.

Successful treatment of streptococcal toxic shock syndrome complicated by primary peritonitis and bilateral empyema in a healthy young woman: Identification of uncommon clone emm103 and novel sequence type 1363

Streptococcal toxic shock syndrome (STSS) has a dramatic clinical course and high mortality rate. Here, we report a case of STSS complicated by primary peritonitis and bilateral empyema. A previously healthy young woman was diagnosed with STSS complicated by primary peritonitis and bilateral empyema. Blood culture results on admission were negative. Sever shock, respiratory failure, systemic inflammation, thrombocytopenia, renal failure, ascites, and pleural effusion occurred, mimicking thrombocytopenia, anasarca, fever, reticulin fibrosis/renal failure and organomegaly (TAFRO) syndrome. Retesting blood cultures identified Streptococcus pyogenes. Gram staining of ascites and pleural fluid indicated gram-positive cocci in chains. Antibiotics, immunoglobulins, and surgical intervention led to recovery without complications. Ex-post genotypic analyses showed uncommon emm103.0 (cluster E3) of emm long sequence (784 base) and novel sequence type 1363. STSS diagnosis can be difficult as it mimics other systemic inflammatory diseases. Therefore, it is crucial for clinicians to perform microbiological examinations from infection foci, even if the initial culture is negative.

Comparing Genomic Characteristics of Streptococcus pyogenes Associated with Invasiveness over a 20-year Period in Korea

Background

Few studies have investigated the invasiveness of Streptococcus pyogenes based on whole-genome sequencing (WGS). Using WGS, we determined the genomic features associated with invasiveness of S. pyogenes strains in Korea.

Methods

Forty-five S. pyogenes strains from 1997, 2006, and 2017, including common emm types, were selected from the repository at Gyeongsang National University Hospital in Korea. In addition, 48 S. pyogenes strains were randomly selected depending on their invasiveness between 1997 and 2017 to evaluate the genetic evolution and the associations between invasiveness and genetic profiles. Using WGS datasets, we conducted virulence-associated DNA sequence determination, emm genotyping, multi-locus sequence typing (MLST), and superantigen gene profiling.

Results

In total, 87 strains were included in this study. There were no significant differences in the genomic features throughout the study periods. Four genes, csn1, ispE, nisK, and citC, were detected only in invasive strains. There was a significant association between invasiveness and emm cluster type A-C3, including, emm1.0, emm1.18, emm1.3, and emm1.76 (P<0.05). The predominant emm1 lineage belonged to ST28. There were no associations between invasiveness and superantigen gene profiles.

Conclusions

This is the first study using WGS datasets of S. pyogenes strains collected between 1997 and 2017 in Korea. Streptococcal invasiveness is associated with the presence of csn1, ispE, nisK, and citC. The emm1 lineage and ST28 clone are explicitly associated with invasiveness, whereas genomic features remained stable over the 20-year period.

Prevalence and identification of antibiotic-resistant scarlet fever group A Streptococcus strains in some pediatric cases at Shenzhen, China

OBJECTIVE

This study aimed to investigate the annual incidence, molecular epidemiological characteristics, and antimicrobial resistance of group A Streptococcus (GAS) clinical isolates from pediatric patients at Shenzhen Children's Hospital during 2016-2020.

METHODS

Clinical samples were collected from pediatric patients with a suspected diagnosis of GAS infections. We studied the annual incidence and characteristics of GAS infections using the GAS antigen detection method. Additionally, 250 GAS isolates were randomly selected for genotyping of the emm gene, and antimicrobial susceptibility assay was performed using the Kirby-Bauer paper dispersion strategy.

RESULTS

Among 43,593 collected samples, 9,313 were positive for the GAS antigen. The main emm type was emm12, followed by emm1, emm6, and emm 4, which were used for distinguishing 90% of the scarlet fever isolated strains. The percentage of emm1 increased from 36% in 2016 to 44% in 2019, whereas the percentage of emm12 decreased from 62% to 50%. Several unusual emm types isolated from scarlet fever patients showed an increase in proportions from 2016 to 2020. These GAS isolates were sensitive to penicillin, ceftriaxone, and vancomycin and were highly resistant to erythromycin and clindamycin.

CONCLUSION

There was a high incidence of GAS infections during 2016-2020 in Shenzhen, China. The GAS isolates had a high resistance rate to erythromycin and clindamycin; penicillin was the antibiotic of choice for GAS infections. The common emm types were emm12 and emm1. Future studies should investigate the clonal structure and superantigen profiles of the population of GAS isolates associated with scarlet fever.

A global snapshot on the prevalent macrolide-resistant emm types of Group A Streptococcus worldwide, their phenotypes and their resistance marker genotypes during the last two decades: A systematic review

Watchful epidemiological surveillance of macrolide-resistant Group A Streptococcus (MRGAS) clones is important owing to the evolutionary and epidemiological dynamic of GAS. Meanwhile, data on the global distribution of MRGAS emm types according to macrolide resistance phenotypes and genotypes are scant and need to be updated. For this, the present systematic review analyses a global set of extensively characterized MRGAS isolates from patients of diverse ages and clinical presentations over approximately two decades (2000 to 2020) and recaps the peculiar epidemiological features of the dominant MRGAS clones. Based on the inclusion and exclusion criteria, 53 articles (3593 macrolide-resistant and 15,951 susceptible isolates) distributed over 23 countries were dissected with a predominance of high-income countries over low-income ones. Although macrolide resistance in GAS is highly variable in different countries, its within-GAS distribution seems not to be random. emm pattern E, 13 major emm types (emm12, 4, 28, 77, 75, 11, 22, 92, 58, 60, 94, 63, 114) and 4 emm clusters (A-C4, E1, E6, and E2) were significantly associated with macrolide resistance. emm patterns A-C and D, 14 major emm types (emm89, 3, 6, 2, 44, 82, 87, 118, 5, 49, 81, 59, 227, 78) and 3 well-defined emm clusters (A-C5, E3, and D4) were significantly associated with macrolide susceptibility. Scrutinizing the tendency of each MRGAS emm type to be significantly associated with specific macrolide resistance phenotype or genotype, interesting vignettes are also unveiled. The 30-valent vaccine covers ~95% of MRGAS isolates. The presented data urge the importance of comprehensive nationwide sustained surveillance of MRGAS circulating clones particularly in Low and Middle income countries where sampling bias is high and GAS epidemiology is obfuscated and needs to be demystified.

Distribution of emm types and macrolide resistance determinants among group A streptococci in the Middle East and North Africa region

OBJECTIVES

The aim of this review was to provide an updated scenario on the epidemiology of group A streptococci (GAS) in the Middle East and North Africa (MENA) region with a special spotlight on the most prevalent emmtypes and macrolide resistance profiles.

METHODS

This review briefly summarises the disease burden for GAS in the MENA region.

RESULTS

Whilst the burden of invasive GAS infections is difficult to assess in the MENA region, the GAS prevalence ranged from 2.5% up to 42.4% in pharyngitis patients and from 2.4% up to 35.4% in healthy carriers.emm1, emm12, emm89, emm4, emm28 and emm3were responsible for the major GAS burden in the MENA region. The coverage rate of the new M protein-based vaccine candidate (30-valent) varied from 42% to 100% according to the country. The rate of erythromycin resistance differed substantially between countries from low to moderate or high.

CONCLUSION

These data add more shreds of evidence on the neglected GAS burden in the MENA region. Systematic surveillance of invasive GAS infections along with molecular characterisation of GAS isolates are strongly recommended to track the trends of circulating clones and to evaluate the potential coverage of vaccine candidates.

Predominance of emm4 and antibiotic resistance of Streptococcus pyogenes in acute pharyngitis in a southern region of Korea

BACKGROUND

Streptococcus pyogenes is the most common cause of bacterial pharyngitis. Genotyping of emm is useful for molecular epidemiological survey of S. pyogenes. Antibiotic resistance data are needed for empirical treatments.

METHODS

In total, 358 children in Changwon, Korea who had pharyngitis symptoms were subjected to throat cultures to isolate S. pyogenes in 2017. emm genotyping was performed by direct sequencing. An antibiotic susceptibility test was performed using the disk diffusion method for erythromycin (ERY), clindamycin (CLI), tetracycline (TET) and ofloxacin (OFX). Screening for macrolide resistance phenotype and its determinants was performed for the ERY-resistant strains.

RESULTS

A total of 190 strains (53.1 %) of S. pyogenes were isolated from 358 children. The most frequent emm genotype was emm4 (53.2 %), followed by emm89 (12.6 %), emm28 (11.6 %) and emm1 (10 %). Antibiotic resistance rates to ERY, CLI, TET and OFX were 3.2 %, 2.6 %, 1.1 % and 2.6%, respectively. There were five isolates of the cMLSB phenotype having the ermB gene and one M phenotype harbouring the mefA gene.

CONCLUSIONS

The distribution of emm genotypes was quite different from those previously reported in Korea. emm4 accounted for more than 50  % of the genotypes. Macrolide resistance rates remained very low, but five of six ERY-resistant strains displayed the cMLSB phenotype.

Molecular Epidemiological Features and Antibiotic Susceptibility Patterns of Streptococcus dysgalactiae subsp. equisimilis Isolates from Korea and Japan

BACKGROUND

The molecular characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) has not yet been performed in Korea. This study aimed to find the differences or similarities in the clinical features, molecular epidemiological findings, and antimicrobial resistance patterns of SDSE from two countries (Korea and Japan).

METHODS

SDSE isolates were collected from Korea (N=69) from 2012-2016 and Japan (N=71) from 2014-2016. Clinical characteristics, emm genotypes, and sequence types (STs) were compared. Microdilution tests were performed using different antimicrobials, and their resistance determinants were screened.

RESULTS

Median ages were 69 years in Korea and 76 years in Japan. The most common underlying diseases were diabetes and malignancy. Blood-derived isolates comprised 36.2% and 50.7% of Korean and Japanese isolates, respectively; mortality was not different between the two groups (5.8% vs 9.9%, P=0.53). Among Korean isolates with 20 different combined ST-emm types, ST127-stG245 (N=16), ST128-stG485 (N=10), and ST138-stG652 (N=8) were prevalent. Among Japanese isolates with 29 different combined types, ST17-stG6792 (N=11), ST29-stG485 (N=7), and ST205-stG6792 (N=6) were prevalent. Resistance rates to erythromycin, clindamycin, and minocycline were 34.8%, 17.4%, and 30.4% in Korea and 28.2%, 14.1%, and 21.4% in Japan, respectively.

CONCLUSIONS

SDSE infections commonly occurred in elderly persons with underlying diseases. There was a significant difference in the distribution of ST-emm types between the two countries. Antimicrobial resistance rates were comparable with different frequencies of resistance determinants in each country.

Distribution of macrolide resistance mechanisms in Bulgarian clinical isolates of Streptococcus pyogenes during the years of 2013-2016

Streptococcus pyogenes, or group A streptococcus (GAS), is the main etiological agent of bacterial tonsillopharyngitis and a common cause of a wide variety of other mild to severe infections.

OBJECTIVES

Objectives of the present study was to determine and evaluate the distribution of genetic mechanisms associated with certain phenotypes of macrolide resistance in Bulgarian GAS isolated during the years of 2013-2016.

METHODS

All GAS strains were screened for the macrolide resistance genes erm(A), erm(B) and mef(A), using multiplex polymerase chain reaction (PCR). The minimal inhibitory concentrations (MICs) of erythromycin, azithromycin, clarithromycin, clindamycin were determined by E-tests.

RESULTS

Almost 23% of GAS isolates obtained in 2013-2014 and near 40% of them in 2015-2016 contained various elements of resistance. The predominant gene was mef(A), which encodes an efflux pump (M-phenotype), identified in 57.84% of the macrolide-resistant strains. The next frequently prevalent mechanism was a combination of mef(A) and erm(B) in 22.55%, which determined high-level inducible or constitutive resistance to macrolides, lincosamides and streptogramins (iMLSB or cMLSB). The highest MIC value (>256mg/L) was detected in association with erm(B) (p<0.05). The MIC range was observed to be much higher in the isolates with combinations of resistance genes vs. those with mef genes alone (p<0.05).

CONCLUSION

The data about the distribution and prevalence of macrolide resistance mechanisms obtained in this study can help in the treatment of persistent and recurrent GAS infections and in the correct choice of empiric therapy.

Pleural empyema and streptococcal toxic shock syndrome due to Streptococcus pyogenes in a healthy Spanish traveler in Japan

Group A Streptococcus (GAS, Streptococcus pyogenes) causes invasive infections including streptococcal toxic shock syndrome (STSS) and local infections. To our knowledge, this is the first report of a case of an invasive GAS infection with pneumonia and pleural empyema (PE) followed by STSS (disseminated intravascular coagulation [DIC] and acute renal insufficiency) in a healthy male adult. He received combined supportive therapies of PE drainage, anti-DIC agent, hemodialysis, and antimicrobials and eventually made a clinical recovery. GAS isolated from PE was found to have emm1/speA genes, suggestive of a pathogenic strain. Clinicians should be aware of the possibility of this disease entity (pneumonia, PE, and STSS) in healthy male adults as well as children and adult women.

Prevalence of M75 Streptococcus pyogenes Strains Harboring slaA Gene in Patients Affected by Pediatric Obstructive Sleep Apnea Syndrome in Central Italy

Recently we reported an association between pediatric obstructive sleep apnea syndrome (OSAS) and Group A streptococcus (GAS) sub-acute chronic tonsil colonization. We showed that GAS may contribute to tonsil hyperplasia via a streptolysin O (SLO)-dependent cysteinyl leukotrienes (CysLTs) production, which can trigger T and B cell proliferation. In the present study, we characterized the GAS strains isolated from pediatric OSAS patients in comparison with a panel of age and sex matched GAS strains unrelated to OSAS, but isolated in the same area and during the same period ranging from 2009 to 2013. We found that slaA gene, previously reported to be associated to CysLTs production pathway, was significantly associated to GAS OSAS strains. Moreover, the most numerous group (32%) of the GAS OSAS strains belonged to M75 type, and 6 out of 7 of these strains harbored the slaA gene. Multilocus Sequence Typing (MLST) experiments demonstrated that the clone emm75/ST49/ smeZ, slaA was associated to OSAS cases. In conclusion, we found an association between slaA gene and the GAS OSAS strains, and we showed that the clone emm75/ST49 harboring genes smeZ and slaA was exclusively isolated from patients affected by OSAS, thus suggesting that this genotype might be associated to the pathogenesis of OSAS, although further studies are needed to elucidate the possible role of SlaA in tonsil hypertrophy development.

A case of descending mediastinitis caused by Streptococcus pyogenes harboring genotype emm25 and sequence type 660

Descending mediastinitis caused by Streptococcus pyogenes (group A streptococcus, GAS) is rare among cases of invasive GAS infection. In this report, we describe a case of a cervical abscess and secondary descending mediastinitis in a previously healthy 39-year-old Japanese man. The patient presented with a 2-week history of a sore throat, and subsequently developed an abscess and descending mediastinitis. We treated the cervical abscess using ampicillin/sulbactam and drainage, and GAS was subsequently isolated in two blood cultures from the patient's admission. Microbiological analyses revealed that the isolate harbored genotype emm25 and sequence type (ST) 660. This strain was susceptible to erythromycin (minimum inhibitory concentration [MIC]: ≤0.12 μg/mL), resistant to minocycline (MIC: >4 μg/mL), and possessed the tet(M) determinant. Although we have reviewed the literature regarding the clinical and microbiological characteristics of descending mediastinitis cause by GAS, little is known regarding epidemiological and clinical characteristics of emm25/ST660 GAS. Furthermore, to best of our knowledge, this is the first reported case of descending mediastinitis caused by emm25/ST660 GAS. Therefore, physicians should be aware of case with a cervical abscess and secondary descending mediastinitis caused by GAS infection, even if the patient is immunocompetent.

Molecular characterization and evaluation of the emerging antibiotic-resistant Streptococcus pyogenes from eastern India

Background

Group A Streptococcus strains causing wide variety of diseases, recently became noticeable in eastern India, are not amenable to standard treatment protocol thus enhancing the possibility of disease morbidity by becoming antibiotic resistance.

Methods

The association of Lancefield group A Streptococcal variation with degree of vir architectural diversity was evaluated using emm typing and restriction fragment length polymorphism analyses. The antibiotic sensitivity patterns were examined by modified Kirby-Bauer method of disk diffusion. Percentage calculations, 95% confidence interval and one-way ANOVA were used to assess differences in proportions.

Results

Our observations revealed 20 different emm types and 13 different HaeIII vir typing patterns. A 1.2 kb fragment was found in all HaeIII typing pattern. Fragments of 1.2 kb and 550 bp were conserved in majority of the isolates. HinfI digestion was found proficient in differentiating the strains of same vir typing patterns. Strong predominance of speC (85%) and speF (80%) genes have been observed encoding exotoxins production. 4 isolates were found to be erythromycin resistant and were of genotype emm49. High degree of tetracycline resistance was shown by 53.57% isolates which belonged to 12 different emm genotypes.

Conclusions

These findings suggested that in addition to emm typing, sequential application of HaeIII and HinfI restriction enzymes in vir typing analysis is an effective tool for group A streptococcal molecular characterization associated with antibiotic resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-2079-9) contains supplementary material, which is available to authorized users.

Characteristics of mucoid Streptococcus pyogenes isolated from two patients with pneumonia in a local community

Streptococcus pyogenes (Group A Streptococcus, GAS) infections can develop into life-threatening disorders. However, the occurrence of some GAS pneumonia cases is relatively rare in a local community. We report here characteristics of mucoid GAS isolates obtained from the sputum of two patients with pneumonia in a local community. Although case-patients did not have contact with each other, case-patient 1′s child and case-patient 2′s grandchild attended the same kindergarten where a GAS pharyngitis epidemic had occurred. We conducted phenotypic and genotypic analyses with the GAS isolates from sputum of both patients, to examine (1) colony appearance between the isolates, (2) numerical profile based on API-20 Strep system, (3) similarity to the type strain using 16S rRNA sequencing, (4) emm type (subtype) and emm full-length sequence, (5) sequence type, (6) sic allele, (7) antimicrobial susceptibility result and the resistance determinant, (8) genome profile following a random amplified polymorphic DNA fragments, and (9) pattern of digested DNA fragments by pulse-field gel electrophoresis. These phenotypic and genotypic analyses revealed similar matching between the isolates from both cases. Our findings suggest that when clinicians examine adult patients having infection with the mucoid GAS, they should confirm whether anyone within the same household also developed the infection and need to investigate epidemic situations in local communities, including kindergartens and elementary schools.