Antimicrobial susceptibility patterns, emm type distribution and genetic diversity of Streptococcus pyogenes recovered in Brazil

A Review of the Impact of Streptococcal Infections and Antimicrobial Resistance on Human Health

Streptococcus pneumoniae, Streptococcus pyogenes (GAS), and Streptococcus agalactiae (GBS) are bacteria that can cause a range of infections, some of them life-threatening. This review examines the spread of antibiotic resistance and its mechanisms against antibiotics for streptococcal infections. Data on high-level penicillin-resistant invasive pneumococci have been found in Brazil (42.8%) and Japan (77%). The resistance is caused by mutations in genes that encode penicillin-binding proteins. Similarly, GAS and GBS strains reported from Asia, the USA, and Africa have undergone similar transformations in PBPs. Resistance to major alternatives of penicillins, macrolides, and lincosamides has become widespread among pneumococci and streptococci, especially in Asia (70-95%). The combination of several emm types with erm(B) is associated with the development of high-level macrolide resistance in GAS. Major mechanisms are ribosomal target modifications encoded by erm genes, ribosomal alterations, and active efflux pumps that regulate antibiotic entry due to mefA/E and msrD genes. Tetracycline resistance for streptococci in different countries varied from 22.4% in the USA to 83.7/100% in China, due to tet genes. Combined tetracycline/macrolide resistance is usually linked with the insertion of ermB into the transposon carrying tetM. New quinolone resistance is increasing by between 11.5 and 47.9% in Asia and Europe. The mechanism of quinolone resistance is based on mutations in gyrA/B, determinants for DNA gyrase, or parC/E encoding topoisomerase IV. The results for antibiotic resistance are alarming, and urgently call for increased monitoring of this problem and precautionary measures for control to prevent the spread of resistant mutant strains.

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.

An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics

Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.

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.

Antimicrobial Resistance among Beta-Hemolytic Streptococcus in Brazil: An Overview

Streptococcus pyogenes, Streptococcus agalactiae and Streptococcus dysgalactiae subsp. equisimilis (SDSE) are the beta-hemolytic streptococci species with the most clinical relevance to humans. These species are responsible for several infections, ranging from mild to life-threatening diseases. Although resistance to recommended drugs has not been so critical as detected in other species, it has occurred in diverse regions. In Brazil, it is possible to observe an increasing macrolide and lincosamide resistance trend due to the spread of polyclonal strains. Macrolide-lincosamide-streptogramin B (MLS) resistance phenotypes have been prevalent among S.&nbsp;agalactiae and S.&nbsp;pyogenes, while M phenotype (resistance only to macrolides) has prevailed among SDSE resistant isolates. Fluoroquinolone resistance is rare in this country, reported only in S.agalactiae and S.pyogenes. This is due to nucleotide substitutions in gyrA and parC genes. Reduced penicillin susceptibility and vancomycin resistance, detected in other regions, have not yet been reported in Brazil. Tetracycline is not a therapeutical option, and resistance has occurred at high levels, especially among S.agalactiae. These findings highlight the need for continuous monitoring in order to track the occurrence of antimicrobial resistance among beta-hemolytic streptococci species circulating in this country.

The Place of Group A Streptococci in Moroccan Children with Pharyngitis and Emm Type Distribution

Background: Streptococcus pyogenes is responsible for a wide variety of diseases, including noninvasive and severe invasive infections. The emm gene encodes the M protein that is the virulence factor and immunological determinant of group A streptococci. Emm typing is the group A Streptococci (GAS) standard molecular typing method based on the amplification of the N terminal hypervariable region of the emm gene. Objectives: The aim of the present study was to determine the prevalence of GAS in children with pharyngitis and determine different types of emm gene in the GAS isolates using emm typing. Methods: The study was carried out over a period of 14 months (from February 2017 to March 2018). Throat samples were collected from cases aged ≤ 18 years with pharyngitis referring to a primary health care center in Fez, Morocco. GAS isolates were subjected to conventional tests to confirm species identification. Antimicrobial susceptibility testing was performed using the standard disk diffusion method. We researched emm gene by a polymerase chain reaction (PCR). Emm types were determined by a sequence-based protocol. Demographic and clinical data were recorded from each patient. Results: From a total of 177 throat samples, 11 isolates (6.2%) were identified as GAS in children with pharyngitis. Antibiotic sensitivity testing revealed that all the GAS isolates were sensitive to penicillin. The sequencing of the PCR products of the emm gene revealed that emm90 was the most obtained emm type (30,77%); while emm75 was the least type observed (7.7%). Conclusions: The emm90 is the most prevalent type detected from patients with tonsillitis. Penicillin and erythromycin are still the foremost effective antibiotics to treat GAS pharyngitis.

Systematic Review and Meta-analysis of the Prevalence of Group A Streptococcal emm Clusters in Africa To Inform Vaccine Development

Low vaccine coverage is of grave public health concern, particularly in developing countries where epidemiological data are often absent. To inform vaccine development for group A Streptococcus (GAS), we report on the epidemiology of the M protein emm clusters from GAS infections in Africa, where GAS-related illnesses and their sequelae, including rheumatic fever and rheumatic heart disease, are of a high burden. This first report of emm clusters across the continent indicates a high probably of coverage by the M protein-based vaccine currently undergoing testing were an emm-cluster based approach to be used.

An emm-cluster based system was proposed as a standard typing scheme to facilitate and enhance future studies of group A Streptococcus (GAS) epidemiological surveillance, M protein function, and vaccine development strategies. We provide an evidence-based distribution of GAS emm clusters in Africa and assess the potential coverage of the new 30-valent vaccine in terms of an emm cluster-based approach. Two reviewers independently assessed studies retrieved from a comprehensive search and extracted relevant data. Meta-analyses were performed (random-effects model) to aggregate emm cluster prevalence estimates. Eight studies (n = 1,595 isolates) revealed the predominant emm clusters as E6 (18%; 95% confidence interval [CI], 12.6% to 24.0%), followed by E3 (14%; 95% CI, 11.2% to 17.4%) and E4 (13%; 95% CI, 9.5% to 16.0%). There was negligible variation in emm clusters with regard to regions, age, and socioeconomic status across the continent. Considering an emm cluster-based vaccine strategy, which assumes cross-protection within clusters, the 30-valent vaccine currently in clinical development would provide hypothetical coverage to 80.3% of isolates in Africa. This systematic review indicates the most predominant GAS emm cluster in Africa is E6 followed by E3, E4, and D4. The current 30-valent vaccine would provide considerable coverage across the diversity of emm cluster types in Africa. Future efforts could be directed toward estimating the overall potential coverage of the new 30-valent vaccine based on cross-opsonization studies with representative panels of GAS isolates from populations at highest risk for GAS diseases.

IMPORTANCE Low vaccine coverage is of grave public health concern, particularly in developing countries where epidemiological data are often absent. To inform vaccine development for group A Streptococcus (GAS), we report on the epidemiology of the M protein emm clusters from GAS infections in Africa, where GAS-related illnesses and their sequelae, including rheumatic fever and rheumatic heart disease, are of a high burden. This first report of emm clusters across the continent indicates a high probably of coverage by the M protein-based vaccine currently undergoing testing were an emm-cluster based approach to be used.

Molecular epidemiology and antimicrobial resistance of group a streptococcus recovered from patients in Beijing, China

BACKGROUND

Group A streptococcus (GAS) is an important human pathogen responsible for a broad range of infections. Epidemiological surveillance has been crucial to detect changes in the geographical and temporal variation of the disease pattern. The objective of this study was to investigate the molecular epidemiological characteristics and antimicrobial resistance of GAS isolates from patients in Children's Hospital in Beijing.

METHODS

From 2016 to 2017, pharyngeal swab samples were collected from the outpatients in Children's Hospital, Capital Institute of Pediatrics, who were diagnosed with scarlet fever. Antimicrobial susceptibility test was performed according to the distribution of conventional antibiotics and Clinical and Laboratory Standards Institute (CLSI) recommendations. The distribution of the macrolide-resistance genes (ermB, ermA, mefA), emm (M protein-coding gene) typing, and superantigens (SAg) gene profiling were examined by polymerase chain reaction (PCR).

RESULTS

A total of 297 GAS isolates were collected. The susceptibility of the isolates to penicillin, ceftriaxone, and levofloxacin was 100%. The resistance rate to erythromycin and clindamycin was 98.3 and 96.6%, respectively. The dominant emm types were emm12 (65.32%), emm1 (27.61%), emm75 (2.69%), and emm89 (1.35%). Of the 297 isolates, 290 (97.64%) carried the ermB gene, and 5 (1.68%) carried the mefA gene, while none carried the ermA gene. The most common superantigen genes identified from GAS isolates were smeZ (96.97%), speC (92.59%), speG (91.58%), ssa (85.52%), speI (54.55%), speH (52.19%), and speA (34.34%). Isolates with the genotype emm1 possessed speA, speC, speG, speJ, speM, ssa, and smeZ, while emm12 possessed speC, speG, speH, speI, speM, ssa, and smeZ superantigens.

CONCLUSIONS

The prevalent strain of GAS isolates in Beijing has a high resistance rate to macrolides; however, penicillin can still be the preferred antibiotic for treatment. Erythromycin resistance was predominantly mediated by ermB. The common emm types were emm12 and emm1. There was a correlation between emm and the superantigen gene. Thus, long-term monitoring and investigation of the emm types and superantigen genes of GAS prevalence are imperative.

Trend of antibiotic susceptibility of Streptococcus pyogenes isolated from respiratory tract infections in tertiary care hospital in south Karnataka

BACKGROUND AND OBJECTIVES

Streptococcus pyogenes is recognized as an important pathogen of respiratory tract infections. The rapidly, emerging problem of antibiotic resistant Streptococcus pyogenes is a major issue nowadays. The present study aimed to evaluate the antibiotic susceptibility of Streptococcus pyogenes isolated from upper respiratory tract infections in tertiary care hospital of south Karnataka.

MATERIALS AND METHODS

A retrospective study was conducted over a period of two years. The specimens were processed by Gram staining and aerobic culture. The bacteria were isolated as per standard protocols. The minimum inhibitory values and extent of antibiotic resistance of commonly used antimicrobials were analysed for the isolated strains.

RESULTS

A total of 2123 specimens were received from patients with respiratory tract infections, among which, 50 Streptococcus pyogenes isolates were obtained. Out of these, 8% were not sensitive to penicillin. Using VITEK 2 system, the prevalence of resistances to cefotaxime, erythromycin, tetracycline, levofloxacin, clindamycin and ceftriaxone were 4.2%, 83%, 51%, 8.9%, 40% and 5.3% respectively.

CONCLUSION

It is important to know about the prevalence of resistance and rising MIC values of commonly used antibiotics regarding Streptococcus pyogenes to avoid therapeutic failures.

Epidemiology of invasive group A streptococcal infections in Norway 2010-2014: A retrospective cohort study

Streptococcus pyogenes or group A streptococcus (GAS) causes mild to severe infections in humans. GAS genotype emm1 is the leading cause of invasive disease worldwide. In the Nordic countries emm28 has been the dominant type since the 1980s. Recently, a resurgence of genotype emm1 was reported from Sweden. Here we present the epidemiology of invasive GAS (iGAS) infections and their association with emm-types in Norway from 2010-2014. We retrospectively collected surveillance data on antimicrobial susceptibility, multilocus sequence type and emm-type, and linked them with demographic and clinical manifestation data to calculate age and sex distributions, major emm- and sequence types and prevalence ratios (PR) on associations between emm-types and clinical manifestations. We analysed 756 iGAS cases and corresponding isolates, with overall incidence of 3.0 per 100000, median age of 59 years (range, 0-102), and male 56 %. Most frequent clinical manifestation was sepsis (49 %) followed by necrotizing fasciitis (9 %). Fifty-two different emm-types and 67 sequence types were identified, distributed into five evolutionary clusters. The most prevalent genotype was emm1 (ST28) in all years (range, 20-33 %) followed by 15 % emm28 in 2014. All isolates were susceptible to penicillin, 15 % resistant to tetracycline and <4 % resistant to erythromycin. A PR of 4.5 (95 % CI, 2.3-8.9) was calculated for emm2 and necrotizing fasciitis. All emm22 isolates were resistant to tetracycline PR 7.5 (95 % CI, 5.8-9.9). This study documented the dominance of emm1, emergence of emm89 and probable import of tetracycline resistant emm112.2 into Norway (2010-2014). Genotype fluctuations between years suggested a mutual exclusive dominance of evolutionary clades.

Antimicrobial susceptibility and genetic relationships among Streptococcus dysgalactiae subsp. equisimilis isolates in Rio de Janeiro

BACKGROUND

Streptococcus dysgalactiae subsp. equisimilis (SDSE) has been increasingly associated with several infectious diseases, ranging from pharyngitis to life-threatening conditions, such as necrotizing fasciitis and streptococcal toxic shock syndrome. However, its molecular epidemiology in some geographical areas remains unclear.

METHODS

In this study, 44 isolates of SDSE, recovered from noninvasive infections (37) and from carriage (7), during 2008-2013, were submitted to antimicrobial susceptibility testing, emm typing and pulsed-field gel electrophoresis (PFGE) analysis.

RESULTS

All isolates were susceptible to ceftriaxone, levofloxacin, penicillin G and vancomycin. Resistance rates to erythromycin was 18.2% and to clindamycin was 6.8%, while 38.7% of the isolates were tetracycline non-susceptible. Macrolide resistance phenotypes were M (5 isolates), iMLSB (2) and cMLSB (1), associated with mefA/E, ermA and ermB genotypes, respectively. Seventeen emm types with 21 subtypes were found, but 6 types (stG653.0, stC1400.0 with three subtypes, stC839.0, stC36.0 with two subtypes, stG480.0 and stG840.0) were detected in 70.4% of the isolates. Six new emm subtypes were identified (stC1400.12, stC1400.13, emm152.1, emm152.2, stG652.6 and stG6792.5). Twenty-five PFGE profiles were obtained from 39 isolates.

CONCLUSIONS

Congruence between both typing systems was observed, since the majority of isolates belonging to a given emm type clustered together by PFGE. Clones (at least 80% similarity) were also observed among isolates with different emm types, probably due to horizontal recombination of the emm gene. Erythromycin-resistant isolates harbored diverse emm genes and generated different PFGE profiles, showing a polyclonal dissemination of such characteristic among SDSE isolates.

Prevalence of the M Protein Gene in Group C and Group G Streptococci Isolated from Patients in Thailand

We surveyed group C and group G β-hemolytic streptococci for emm and emmL (emm -like) genes which encode the M protein, as well as determined their antimicrobial susceptibilities. A total of 97 isolates 79 GCS/GGS isolates and 18 isolates from other groups were tested for the M protein gene by PCR. Focusing on invasive infections with group A (GAS), group C (GCS), and group G (GGS) β-hemolytic streptococci isolated from blood, the M protein gene was found in 90.0%, 84.6%, and 78.3% of isolates, respectively. The hypervariable N terminal region of the emm was sequenced from 62 isolates, and 26 types of the emm gene were identified. Based on these results, type emm222.2 may be endemic to Thailand. The results of antimicrobial susceptibility testing of groups C, G, and non-groups A to G isolates indicated high susceptibility (range 82-100%) to penicillin, cefotaxime, chloramphenicol, clindamycin, erythromycin, linezolid, ofloxacin, and vancomycin, whereas the isolates showed low susceptibility (range 0-15.6%) to tetracycline.

Macrolide-resistant Streptococcus pyogenes: prevalence and treatment strategies

Although penicillin remains the first-choice treatment for Streptococcus pyogenes infection, macrolides are important alternatives for allergic patients and lincosamides are recommended together with β-lactams in invasive infections. S. pyogenes may exhibit macrolide resistance because of active efflux (mef genes) or target modification (erm genes), the latter conferring cross resistance to lincosamides and streptogramin B. Worldwide, resistance is restricted to a limited number of genetic lineages, despite resistance genes being encoded on mobile genetic elements. For reasons that are not completely clear, resistance and the associated phenotypes are highly variable across countries. Although resistance remains high in several countries, particularly in Asia, an overall decreasing trend of resistance has been noted in recent years, mostly in Europe. This decrease is not always accompanied by declines in macrolide consumption, suggesting significant roles of other factors in determining the dynamics of macrolide-resistant clones. Continued surveillance is needed to obtain further insights into the forces governing macrolide resistance in S. pyogenes.