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Antimicrob Agents Chemother. Apr 2007; 51(4): 1228–1233.
Published online Jan 22, 2007. doi:  10.1128/AAC.01054-06
PMCID: PMC1855467

Phenotypic and Genotypic Characterization of Streptococcus pyogenes Isolates Displaying the MLSB Phenotype of Macrolide Resistance in Spain, 1999 to 2005[down-pointing small open triangle]

Abstract

The aim of this study was to describe the genetic characteristics of Streptococcus pyogenes showing the MLSB phenotype of macrolide resistance from 1999 to 2005 in Spain and to highlight the substantial increase in these isolates in the last few years. The antimicrobial susceptibilities of 17,232 group A streptococci isolated from Madrid and Gipuzkoa from 1999 to 2005 were studied. The presence of the resistance genes ermA, ermB, mef, tetM, and tetO and the presence of the intTn and xis genes of the Tn916-Tn1545 transposon family were studied in a sample of 739 MLSB-resistant isolates. The epidemiological relationships among these isolates were analyzed by emm typing, T typing, and multilocus sequence typing. Erythromycin resistance was found in 21.3% of the isolates analyzed (annual variation of 14.3% to 28.9%). Until 2003, most erythromycin-resistant isolates showed the M phenotype, but in 2004 and 2005, about 50% of isolates showed the MLSB phenotype. Among the MLSB-resistant isolates studied, 16 clones were identified. The most prevalent clone was a strange emm11/T11/ST403 clone with a null yqiL allele. All but one of the 463 emm11/T11/ST403 isolates carried the ermB, tetM, intTn, and xis genes. The second most prevalent MLSB-resistant clone was emm28/T28/ST52, which comprised two subclones: one bacitracin-resistant, tetracycline-susceptible subclone carrying the ermB gene (n = 115) and another bacitracin-susceptible, tetracycline-resistant subclone carrying the ermB and tetM genes (n = 33). The rapid diffusion of these two clones, and especially of emm11/T11/ST403, caused the large increase in MLSB-resistant S. pyogenes isolates in Spain, suggesting a potential ability for international dissemination.

Streptococcus pyogenes is a pathogen with worldwide distribution that causes a broad spectrum of infections, from uncomplicated pharyngitis to severe life-threatening infections (6). In the absence of a β-lactam allergy, the treatment of choice is penicillin, while the first-line alternative treatments are macrolides or lincosamides. There are two main phenotypes of macrolide resistance: the M phenotype, mediated by the mef genes (8), which confer low-level resistance to 14- and 15-membered macrolides but not to 16-membered macrolides, lincosamides, or streptogramin B, and the MLSB phenotype, mediated by the erm genes (20, 34), which confer resistance to macrolides, lincosamides, and streptogramin B antimicrobial agents. This latter phenotype can be constitutive, generally mediated by the ermB gene, or inducible, generally mediated by the ermA subclass TR (ermA) gene (31). Other mechanisms of resistance to macrolides or lincosamides in S. pyogenes (e.g., mutations in ribosomal proteins) are infrequently involved and currently have little clinical impact (4, 17).

The factor most directly associated with the increase in antimicrobial resistance is the high level of antibiotic consumption among the population (2, 15). Nonetheless, the final cause of a higher or lower prevalence of antimicrobial resistance depends on the circulating clones.

The aim of this study was to highlight the substantial increase in the MLSB phenotype of macrolide resistance in S. pyogenes strains isolated in the last few years in Spain and to describe the genetic characteristics of these isolates.

MATERIALS AND METHODS

The province of Gipuzkoa (whose capital is Donostia-San Sebastián) is located in the northeastern area of the Basque Country in Spain, bordered by the Bay of Biscay and France to the north; Madrid is located in the center of Spain (415 km from San Sebastián).

All group A streptococci (GAS) isolated at the Microbiology Department of Hospital Donostia (Gipuzkoa) and in the Centro de Salud de Argüelles (Madrid) between 1999 and 2005 were included in this study. During the 7 years of the study, 17,232 GAS isolates (8,772 from Madrid and 8,460 from Gipuzkoa) were tested for antimicrobial susceptibility. More than 85% of the isolates were obtained from the pharyngeal tract.

Clinical isolates were characterized as being GAS according to their colony morphology, beta-hemolysis on blood agar, bacitracin susceptibility, and/or coagglutination with specific antisera (Slidex, Streptokit; bioMérieux, Marcy l'Etoile, France). GAS were confirmed as being S. pyogenes by the commercially available identification system Rapid ID 32 STREP (bioMérieux, Marcy l'Etoile, France).

Antimicrobial susceptibility testing was performed by the broth microdilution method using Sensititre microtiter trays (Trek Diagnostics Systems, West Sussex, England) and cation-adjusted Mueller-Hinton broth supplemented with 3 to 5% lysed horse blood. The results were interpreted according to CLSI (formerly NCCLS) criteria (9). Staphylococcus aureus ATCC 29213 was used as the control. To expand the range of dilutions available in the broth microdilution trays, Etest strips (AB Biodisk, Solna, Sweden) were used. Inducible resistance was classified on the basis of a double-disk test with erythromycin (15 μg) and clindamycin (2 μg) disks (Bio-Rad, Marnes-la-Coquette, France).

Molecular detection of erythromycin resistance genes and typing methods were performed using a sample of 739 MLSB-resistant randomly selected isolates (284 from Madrid and 455 from Gipuzkoa). This sample represented 55.7% of all MLSB-resistant isolates obtained during the study period.

Detection of macrolide resistance genes (mef, ermA, and ermB), tetracycline resistance genes (tetM and tetO), and the intTn and xis genes of the Tn916-Tn1545 transposon family was performed by PCR using the primers described in Table Table1.1. Determinants of resistance from representative isolates (one to four) of each clone were sequenced and analyzed using BLAST software (available at http://www.ncbi.nlm.nih.gov/BLAST/).

TABLE 1.
PCR primers

T typing was performed by slide agglutination of trypsin-digested suspensions of bacteria with rabbit type-specific antiserum (pharmaSEVAC, Prague, Czech Republic) (18).

emm types were determined according to guidelines of the Division of Bacterial and Mycotic Diseases, Centers for Disease Control and Prevention (available at http://www.cdc.gov/ncidod/biotech/strep/doc.htm).

Multilocus sequence typing (MLST) was performed according to recommendations provided at http://spyogenes.mlst.net.

PCR-RFLP.

To genetically characterize all the isolates and to obviate the need to sequence the emm gene and the seven alleles of the MLST of each isolate, the amplified products of the emm gene were subjected to digestion with the restriction endonucleases HaeIII and MboII. The amplified products of three of the seven housekeeping alleles of MLST (gki, murI, and yqiL) were digested with the enzymes AciI and BsrI, HphI, and NlaIV, respectively. The grouping obtained with the PCR-restriction fragment length polymorphism (RFLP) method was confirmed by sequencing of the emm gene, and the seven alleles of the MLST of each PCR-RFLP pattern were detected. The MLST was assigned by the RFLP method only to isolates previously well characterized by emm type, T type, and genotypic and phenotypic resistance patterns.

The emm gene and the seven alleles of MLST were sequenced in all the isolates of the 10 clones with less than 5 isolates each, in 50% of the isolates of the 2 clones with between 5 and 20 isolates each, and in more than 10% of the isolates of the clones with more than 40 isolates each. Overall, the seven alleles of the MLST were sequenced in 125 isolates.

Pulsed-field gel electrophoresis (PFGE) was performed as previously described (28).

In this work, a clone was defined as a group of isolates showing the MLSB phenotype of resistance with the same emm type, the same sequence type (ST) complex, and a similar T type. In this study, an ST complex describes a group of STs that share six out of the seven MLST loci.

RESULTS

Erythromycin resistance among the GAS isolated between 1999 and 2005 was 21.3% (annual variation of 14.3% to 28.9%) (Fig. (Fig.1).1). The overall percentage of isolates with the MLSB phenotype of resistance increased from 3.3% in 1999 to 10.2% between 2003 and 2005 (7.6 to 13.1%). The annual percentage of isolates with the M phenotype of resistance showed variations through the entire period (6.8 to 19.1%), although the tendency since 2003 was to decrease (Fig. (Fig.11).

FIG. 1.
Annual percentage of isolates (n = 17,232) showing the M (n = 2,356) and MLSB (n = 1,326) resistance phenotypes. The proportional participation of emm11/T11/ST403 and emm28/T28/ST52 clones is illustrated by data extrapolated from ...

Among the 739 S. pyogenes clinical isolates showing the MLSB resistance phenotype studied in depth, 652 isolates carried the ermB gene, 80 carried ermA, three carried both ermB and mef, and one carried both ermA and mef; in the remaining three isolates, neither ermA, ermB, nor mef genes were detected. Overall, the isolates with the ermB gene showed a high level of erythromycin and clindamycin resistance (MIC50, >64 μg/ml) as well as telithromycin resistance (MIC50, >4 μg/ml). The isolates harboring the ermA gene showed moderate erythromycin resistance (MIC50, 4 μg/ml) and, without induction, were susceptible to clindamycin (MIC50, <0.5 μg/ml) and telithromycin (MIC50, <0.25 μg/ml).

Sixteen emm types were detected. Thirteen emm types correlated with an ST, and three correlated with an ST complex. The three ST complexes were as follows: ST20, ST21, and ST403 in the same emm11 type; ST63 and ST369 in the same emm77 type; and ST38 and ST39 in the same emm4 type. In contrast, different emm/ST combinations shared the same T type, and frequently, more than one T type was detected in a single isolate. For the purposes of clarity, each clone was designed with the most prevalent T type found in that clone, although more detailed information is included as a footnote to Table Table22.

TABLE 2.
Annual distribution of 16 clones among a sample of 739 Streptococcus pyogenes isolates with the MLSB-resistant phenotypea

When the STs were combined with the emm and T types, the 739 MLSB-resistant isolates were grouped into 16 clones (Tables (Tables22 and and33).

TABLE 3.
Macrolide and tetracycline determinants of resistance in different clones of Streptococcus pyogenes with the MLSB resistance phenotype

The most frequent clone was emm11/T11/ST403 (ST403-ST20-ST21 complex) whose ST could not initially be determined in most of the isolates because the housekeeping yqiL allele was absent (null yqiL allele). This ST is currently designated ST403. The first isolates of this clone were detected in August 2002, and their rapid dissemination since 2003 has made it the most prevalent clone, with 463 (62.7%) isolates. This clone included 448 ST403 isolates (which did not amplify the yqiL allele), 9 ST21 isolates, and 6 ST20 isolates. Of the seven alleles that define an ST, six are shared by STs 20, 21, and 403, with the noncommon allele being yqiL. The yqiL allele is absent in ST403 and has only two nucleotide differences between ST20 and ST21.

By PFGE, these three STs shared a common profile (pattern similarity of >80%). All these isolates except one carried the ermB, tetM, intTn, and xis genes (Table (Table2),2), suggesting the presence of a Tn1545-like transposon. The remaining isolate showed moderate erythromycin resistance (MIC, 8 μg/ml) and tetracycline susceptibility (MIC, <0.5 μg/ml) and carried the ermA gene.

The second most frequent clone between 1999 and 2005 was emm28/T28/ST52, which included 148 (20%) isolates. All isolates of this clone shared a single T type (T28) and emm type (emm28), but two subpopulations of isolates, designated as subclones in this study, could be differentiated by their phenotypes of resistance and especially by their different bacitracin susceptibilities. One subclone comprised 115 bacitracin-resistant isolates (bacitracin MIC of ≥2 U/ml with no zone of inhibition around a 0.04-U bacitracin disk) that harbored the ermB gene and were tetracycline susceptible. The second subclone comprised 33 emm28/T28/ST52 bacitracin-susceptible isolates, 31 of which were tetracycline resistant and carried the ermB and tetM genes. One of the remaining isolates carried the ermA gene (erythromycin and tetracycline MICs of 2 and <0.25 μg/ml, respectively) and the other carried the ermB gene (erythromycin and tetracycline MICs of >64 and <0.25 μg/ml, respectively).

The third clone in order of frequency was the emm22/T12/ST46 clone, which included 62 isolates, 38 with the ermA gene and 24 with the ermB gene; all the isolates that had the ermA gene were tetracycline susceptible. Ten out of the 24 isolates with the ermB gene were tetracycline resistant and harbored the tetM, intTn, and xis genes.

The fourth most frequent clone was the emm77/T28/ST63 clone (ST63-ST369 complex) (n = 24). Most of the isolates of this clone had the ermA gene (Table (Table2).2). The intTn and xis genes were detected in the single isolate of this clone and carried both the ermB and mef genes. This clone included 23 ST63 isolates and 1 ST369 isolate. ST63 and ST369 have only one nucleotide difference at the yqiL allele, with the sequences of the other six alleles being identical (single-locus variant). The PFGE pattern of the ST369 isolate showed >80% similarity with the patterns of other ST63 isolates. A more detailed description of this clone has previously been described (24).

We also included two emm4/T4 isolates in the same clone (Tables (Tables22 and and3),3), because ST38 and ST39 are differentiated by only one nucleotide at the gtr allele, and both PFGE patterns showed >80% similarity.

DISCUSSION

Macrolides and lincosamides are considered to be a suitable alternative to penicillin in patients who are allergic to penicillin. In animal models, clindamycin has proven to be more effective than penicillin in the treatment of some invasive infections (33) and is the treatment of choice, alone or in combination with penicillin, for sepsis of soft tissue origin (1, 5). When S. pyogenes shows resistance to clindamycin, it nearly always shows a high level of resistance to erythromycin and other macrolides. Consequently, although the M phenotype of resistance is important, the MLSB phenotype of resistance has greater implications by limiting the therapeutic possibilities in cases of infection.

Several reports of the antimicrobial susceptibility of S. pyogenes isolates in Spain from 1984 to 1999 showed that until 1990, erythromycin resistance in S. pyogenes was low (less than 3%). After 1990, resistance increased, reaching 25 to 35% of all S. pyogenes strains isolated in 1995 (15, 27, 29). As in other countries, total macrolide consumption in Spain showed a good correlation with the erythromycin resistance curve (15). Before 1999, the M phenotype predominated among erythromycin-resistant S. pyogenes isolates, representing around 95% of these isolates (15, 27, 29). In the present study, we found that in 1999, the M phenotype was expressed by approximately 85% (340/402) of all erythromycin-resistant isolates. In 2004 and 2005, about 50% of erythromycin-resistant isolates (705/1,368) displayed the MLSB phenotype. Four major clones grouped 94.3% of all S. pyogenes isolates displaying the MLSB phenotype of resistance. In 2003, 2004, and 2005, the emm11/T11/ST403 clone represented 77.4%, 85.6%, and 66.2% of MLSB-resistant isolates, respectively, with similar prevalences in Madrid and in Gipuzkoa. ST403 isolates of this clone are probably the only S. pyogenes strains that do not have one of the seven housekeeping alleles used for MLST.

Although the origin of this clone in Europe is not known, emm11 isolates carrying the ermB gene were frequently isolated in Belgium (22) and France (3) and occasionally in Italy (36). Because the isolates in these studies were characterized by emm typing only (the French isolates by emm and T typing), it cannot be ascertained whether they were of the same type as emm11/T11/ST403 found in Spain.

The emm28/T28/ST52 bacitracin-resistant subclone has persisted in Spain since its appearance in 1999. The characteristic of being bacitracin resistant will hamper its detection in laboratories that use bacitracin susceptibility as a presumptive identification test. emm28/T28/ST52 bacitracin-resistant isolates were first detected in Spain and Portugal in 1999 (28, 32), in France and Belgium between 2000 and 2002 (21, 23), and in the Czech Republic probably in the same period (35), proving its spread through Europe in the last few years.

Tetracycline resistance has been considered to be an important cofactor in the selection of erythromycin resistance (26). Tetracycline resistance in S. pyogenes has been associated with the tetM gene and, less frequently, with the tetO gene (14). In this study, the tetM gene was present in 70.6% of the MLSB-resistant isolates (95.6% of tetracycline-resistant isolates), while the tetO gene was detected exclusively in MLSB-resistant isolates of the emm77/T28/ST63 clone. This clone included 23 ST63 isolates and 1 ST369 isolate.

Most isolates with both the tetM and ermB genes carried the intTn and xis genes. The presence of the intTn and xis genes suggested the existence of a transposon related to the Tn916-Tn1545 family of conjugative transposons. Conjugative transposons from the Tn916-Tn1545 family are found in different species of the genus Streptococcus (7, 10, 30). These elements can carry several determinants of resistance and contribute to the dissemination of multidrug resistance.

Because of the inherent limitations of conventional phenotyping methods for detecting circulating strains, as well as their mechanisms of resistance, molecular techniques that complement the information provided by these methods have been developed. Molecular methods such as MLST, emm typing, and PFGE are highly discriminatory genotypic techniques that provide valuable information for cluster analysis. MLST is an unambiguous sequence-based method that allows the genetic relationship between the organisms of bacterial species to be identified (11). MLST is more highly discriminative than emm typing, and in this study, it was considered more appropriate to reduce its discriminative power and to introduce the concept of the ST complex in the definition of the clone. Since all STs assigned to the same ST complex shared alleles at six of the seven MLST loci and since their PFGE patterns, emm types, T types, and macrolide and tetracycline determinants of resistance showed strong similarity, the different STs assigned to a single ST complex were considered to be minor variants of the same clone.

emm genes encode M proteins that constitute an important virulence factor, and to date, more than 120 emm types have been well characterized (12, 13). Classic M protein serotyping has been replaced with the sequence-based methodology of emm typing. emm typing has enabled new types to be added to the Lancefield scheme. Only recently, the emm94-emm102 types were incorporated (13). In this study, emm94 and emm102 were detected and could not have been M-protein typed using all typing serum stocks available to international GAS reference laboratories (13). Ten out of the 16 emm types found in this study, which grouped more than 95% of all the total MLSB-resistant isolates studied, were targeted by a 26-valent GAS vaccine currently undergoing clinical trials (16).

T serotyping, a phenotypic method, was the less discriminative of all the typing methods used in this study, but as in other studies, it added important information and validated data provided by genotypic methods (19). Moreover, as recently suggested, the induction of a protective immune response against T antigens may be another useful strategy for the development of vaccines against S. pyogenes (25).

The extensive and rapid diffusion of a clone in a specific region is indicative of its high infectious ability, and therefore, it becomes a threat for international dissemination. The advantage of using molecular methods, together with the T serotype, is that comparisons among S. pyogenes isolates from different countries and at different times can easily be made, increasing knowledge of the spread of resistant clones and facilitating future preventive measures.

Acknowledgments

This work was supported in part by two grants from the Fondo de Investigación Sanitaria, Ministry of Health and Consumption, Spain: PI050181 and CIBER B06/06-26.

Footnotes

[down-pointing small open triangle]Published ahead of print on 22 January 2007.

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