rRNA gene restriction patterns of Streptococcus pyogenes: epidemiological applications and relation to serotypes

Development of species-specific primers for detection of Streptococcus pyogenes from throat swabs

A species-specific molecular marker has been developed to detect the human pathogen Streptococcus pyogenes from throat swabs. Streptococcus pyogenes is an important pathogen among Gram-positive organisms. A rapid and simple diagnostic tool is of utmost importance for the identification of this pathogen. The random amplified polymorphic DNA (RAPD) technique was used to differentiate the S. pyogenes strains. A differentially amplified fragment obtained from RAPD profiles was sequenced and characterized, which was developed into a sequence characterized amplified region (SCAR) marker to evaluate the specificity of S. pyogenes from other species of Streptococcus. The sensitivity of the SCAR primers was studied by qualitative PCR and the detection limit was found to be 10(-1) ng of genomic DNA or one to two cells of S. pyogenes. The specificity of the primers was assayed in 270 clinical throat swabs wherein 23 samples turned to be positive, which was highly significant over culture-based methods. This species-specific primer enables accurate detection of S. pyogenes from clinical samples and will be a useful tool in epidemiological studies.

Molecular characterization of invasive and non-invasive Streptococcus pyogenes isolates from Romania

In 2002, the Romanian National Reference Laboratory was invited to join the Strep-EURO project to study invasive Streptococcus pyogenes infections. During 2003 and 2004, a total of 33 isolates recovered from invasive disease were received from eight Romanian counties. For comparison, 102 isolates from non-invasive disease, as well as a collection of 12 old invasive strains (isolated between 1967 and 1980) were included. All isolates were characterized by several methods: T and emm typing, presence of the fibronectin-binding protein F1 gene (prtF1), serum opacity factor (sof), and superantigen (SAg) genes (speA, speB, speC, speF, speG, speH, ssa and smeZ). The recent invasive isolates exhibited 19 emm-types, of which emm1, emm81, emm76, emm49 and emm78 covered 57 % of the strains. Furthermore, multilocus sequence typing analysis revealed nine new sequence types, corresponding to emm types 1, 12, 49, 81, 92, 100, 106 and 119. The non-invasive isolates comprised 24 different emm types with a predominance of emm1 and 12; the old invasive strains were of eight emm types, of which four were unique for this group. All isolates harboured speB and speF; smeZ was detected in all invasive strains, except for the emm49 and emm81 isolates. The majority of isolates from carriers, and patients with pharyngitis were prtF1 positive, most of these (14 strains) being emm12. High tetracycline resistance rates were noted among both invasive and control isolates (54 % and 35 %, respectively), whereas macrolide resistance rates were low (3 % and 5 %, respectively). Active and continuing surveillance is required to provide an accurate assessment of the disease burden and to provide epidemiological data on the character of isolates in Romania.

Epidemiology and molecular characterization of Streptococcus pyogenes recovered from scarlet fever patients in central Taiwan from 1996 to 1999

One hundred seventy-nine Streptococcus pyogenes isolates recovered from scarlet fever patients from 1996 to 1999 in central Taiwan were characterized by emm, Vir, and pulsed-field gel electrophoresis (PFGE) typing methods. The protocols for Vir and PFGE typing were standardized. A database of the DNA fingerprints for the isolates was established. Nine emm or emm-like genes, 19 Vir patterns, and 26 SmaI PFGE patterns were detected among the isolates. Among the three typing methods, PFGE was the most discriminatory. However, it could not completely replace Vir typing because some isolates with identical PFGE patterns could be further differentiated into several Vir patterns. The prevalent emm types were emm4 (n = 81 isolates [45%]), emm12 (n = 64 [36%]), emm1 (n = 14 [8%]), and emm22 (n = 13 [7%]). Some emm type isolates could be further differentiated into several emm-Vir-PFGE genotypes; however, only one genotype in each emm group was usually predominant. DNA from nine isolates was resistant to SmaI digestion. Further PFGE analysis with SgrAI showed that the SmaI digestion-resistant strains could be derived from indigenous strains by horizontal transfer of exogenous genetic material. The emergence of the new strains could have resulted in an increase in scarlet fever cases in central Taiwan since 2000. The emm sequences, Vir, and PFGE pattern database will serve as a basis for information for the long-term evolutionary study of local S. pyogenes strains.

Correlations between molecular subtyping and serotyping of Listeria monocytogenes

To define relationships between Listeria monocytogenes genetic lineages, ribotypes, and serotypes, 235 L. monocytogenes isolates were characterized by serotyping and automated EcoRI ribotyping. Genetic lineage predicted the following serovar clusters: lineage I, comprising serotypes 1/2b, 3b, 3c, and 4b; lineage II, comprising serotypes 1/2a, 1/2c, and 3a; and lineage III, comprising serotypes 4a and 4c. Some EcoRI ribotypes contained multiple serotypes; a subset of these isolates was further differentiated with PvuII ribotyping. Of the 12 resultant EcoRI-PvuII combination types, only 4 contained multiple serotypes, demonstrating the potential of ribotyping for serotype prediction.

Comparison of serotyping, ribotyping and pulsed-field gel electrophoresis for distinguishing group A Streptococcus strains isolated in Albania

Conventional serotyping for T antigens, rRNA gene restriction fragment length polymorphism analysis (ribotyping) and pulsed-field gel electrophoresis were compared for distinguishing among group A streptococci isolated in Albania between 1980-1982 and in 1995. A total of twelve serotypes were identified among seventy GAS strains. Ribotyping revealed eight and eleven distinct patterns after digestion with HindIII and PvuII, respectively. Twenty-three strains of serotype T12 were subdivided in 10 ribotypes and 11 strains of T2 serotype were differentiated in 5 ribotypes. By comparison, PFGE generated 37 patterns after SmaI digestion. The index of discrimination, using the Hunter-Gaston formula, was applied to assess the value of these methods for interpretation of the epidemiological data. For serotyping the value of index was 0.85. The ribotyping system revealed an ID of 0.83 when the combination HindIII and PvuII was used. This index reached 0.97 for PFGE. The methods used were useful to subtype the isolates of GAS.

Convenient and versatile DNA extraction using agarose plugs for ribotyping of problematic bacterial species

We describe a convenient, versatile and safe method for preparing bacterial DNA for ribotyping analysis. In this method, extraction of bacterial DNA from Salmnonella typhi and Burkholderia pseudomallei. and subsequent restriction endonuclease digestion, was performed in agarose blocks/plugs thus minimizing shearing and loss of DNA, problems commonly associated with liquid phase phenol extraction. Digested DNA in the plugs was then electrophoresed directly, transferred to nylon membranes and hybridized with labeled rDNA probes in the usual manner to provide reproducible restriction patterns. This method is particularly useful for bacterial species where standard DNA extraction in the liquid phase using phenol has been problematic (e.g. B. pseudomallei) but can be used for any bacterial species. The DNA extracted within the agarose plugs can be stored for long periods and can be used in other, widely-used typing methods such as pulsed-field gel electrophoresis (PFGE) and PCR-based techniques. Embedding live cells directly in agarose plugs also minimizes the risk of exposure to these virulent human pathogens among laboratory workers.

Survival of oral bacteria

The global distribution of individual species of oral bacteria demonstrates their ability to survive among their human hosts. Such an ubiquitous existence is the result of efficient transmission of strains and their persistence in the oral environment. Genetic analysis has identified specific clones of pathogenic bacteria causing infection. Presumably, these express virulence-associated characteristics enhancing colonization and survival in their hosts. A similar situation may occur with the oral resident flora, where genetic variants may express specific phenotypic characteristics related to survival. Survival in the mouth is enhanced by dental plaque formation, where persistence is associated with the bacteria's capacity not only to adhere and grow, but also to withstand oxygen, wide fluctuations in pH and carbohydrate concentration, and a diverse array of microbial interactions. Streptococcus mutans has been discussed as a 'model' organism possessing the biochemical flexibility that permits it to persist and dominate the indigenous microflora under conditions of stress.

Molecular epidemiology of Streptococcus pyogenes in an area where acute pharyngotonsillitis is endemic

During an open clinical trial in an area where streptococcal infections are hyperendemic, we studied the genetic polymorphism of Streptococcus pyogenes isolates collected from patients and from healthy carriers living in close contact with them. The clonal diversity of isolates was analyzed by pulsed-field gel electrophoresis with three restriction enzymes (SmaI, ApaI, and SacII). The pharynx of each patient and healthy carrier was colonized by a single clone, suggesting the clonal nature of streptococcal colonization in individuals. Among 52 isolates obtained from patients with acute pharyngotonsillitis, we found 14 genetically unrelated clones, showing the genetic diversity of S. pyogenes. However, two clones belonging to the M1 and M12 serotypes represented about 70% of isolates in carriers and patients. Pharyngeal colonization in cured patients was monitored for 3 to 4 months. After the initial elimination of S. pyogenes following antibiotic therapy, the rate of recolonization was high by day 30 (about 20%) and was also at that level between days 90 and 120; this was similar to the carriage rate in family contacts. Thus, cured patients can be recontaminated by unrelated clones, suggesting that colonization of healthy carriers might be a potential source of spread and redistribution of S. pyogenes isolates.

Genotypic and phenotypic diversity of Streptococcus dysgalactiae strains isolated from clinical and subclinical cases of bovine mastitis

This study was conducted to characterize Streptococcus dysgalactiae isolated from cases of bovine mastitis. One hundred strains from 100 dairy herds in Denmark, 29 strains from 29 dairy herds in Pennsylvania, USA, 7 reference strains and 18 strains consisting of 9 paired strains from 9 quarters were investigated using biotyping (utilization of tagatose and sorbitol) and HindIII ribotyping. Four different biotypes were observed. Only 34 of the 100 Danish strains utilized either tagatose or sorbitol, 18 utilized tagatose, 15 sorbitol and 1 both tagatose and sorbitol. In contrast, among the American strains one (3.4%) did neither utilize tagatose or sorbitol, twenty (69.0%) utilized tagatose, four (13.8%) sorbitol and four (13.8%) both tagatose and sorbitol. HindIII ribotyping produced 15 different types among all the strains, 9 different types were found among the Danish strains and 8 types among American strains. Five types were observed among both the Danish and the American strains. The 7 reference strains were assigned to 5 different ribotypes. Three type strains (ATCC 27957, NCTC 4670, NCTC 4335) were assigned to a type that was present among both the Danish and the American strains. Ribotyping was the most discriminatory typing method. Agreement between ribo- and biotyping was observed, and especially pronounced among the Danish strains. The 9 paired strains were in case found to have identical ribo- and biotype.

Molecular subtyping of prevalent M serotypes of Streptococcus pyogenes causing invasive disease

Reproducible methodologies and a scheme for high-resolution genotyping of Streptococcus pyogenes were defined with respect to a study of six predominant M serotypes causing invasive group A streptococcal disease in the United Kingdom. Serotype reference strains were compared with nine clinical isolates of each serotype from patients with diseases such as pneumonia, puerperal sepsis, toxic shock-like-syndrome, cellulitis, or necrotizing fasciitis. Four enzymes were evaluated for their discriminatory power in 16S rRNA gene-specific ribotyping. Discriminatory power was greatest with EcoRI, which generated serotype-specific ribotypes, and with SacI, which could subdivide strains of the same M serotype. Twenty-five combined ribotypes were found among the 60 strains, and the indices of discriminatory power (D values) of this method varied from 0.51 within serotype M1 to 0.98 within strains of serotype M5. Macrorestriction with the rarely cutting endonuclease SmaI and pulsed-field gel electrophoresis gave D values varying from 0.37 within serotype M1 to the maximal 1.0 within serotype M5. Comparison of macrorestriction profiles revealed various degrees of genetic heterogeneity within M serotypes. Strains of M1, M3, M6, and M11 exhibited clonally related macrorestriction profiles, while those of R28 and M5 strains were consistent with polyphyletic origin.