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Antimicrobial Agents and Chemotherapy, May 2009, p. 1921-1925, Vol. 53, No. 5
0066-4804/09/$08.00+0 doi:10.1128/AAC.01065-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Quotient Bioresearch Ltd., Fordham, United Kingdom,1 Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy2
Received 7 August 2008/ Returned for modification 7 November 2008/ Accepted 20 February 2009
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There has been some debate over the nomenclature of the mef gene. Based on the fact that the mef subclasses show
80% homology, it has been suggested that both subclasses should be designated mef(A) (13) with further designation by subclass should the need arise. Klaassen and Mouton have argued the need to identify mef(A) and mef(E) separately due to the fact that each gene originated from a different transposable element, Tn1207.1 and mega, respectively (6), and that the erythromycin MICs associated with mef(A) are higher than the erythromycin MICs associated with mef(E) (1).
In this paper, notation of the mef gene will be done according to its subclass, e.g., mef(A) subclass mef(E) will be represented as mef(E).
Since the discovery of mef(A) and mef(E), further subclasses have been published. The subclass mef(I) was found to be present in S. pneumoniae in the IQ element, which is different from Tn1207.1 and the mega element (11). mef(I) was shown to be 91.4% identical to mef(A) and 93.6% identical to mef(E). Extending this subclass, mef(O) has been described in S. pyogenes, which is 97% identical to the mef gene present in Streptococcus dysgalactiae (15).
In this report, we definitively prove the existence of mef(E) and mef(I) in S. pyogenes and describe a novel subclass and a mosaic variant of mef in S. pyogenes.
(This paper was presented in part at the 47th ICAAC in Chicago, IL.)
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Isolate preparation. All isolates were subcultured from storage (–70°C freezer or plates stored at 4°C) onto horse blood agar and incubated overnight at 36°C in 5 to 6% CO2. An aliquot (100 µl) of RNase/DNase-free H2O (Sigma, Poole, United Kingdom) was added to each of the 96 wells of a MicroAmp plate (Applied Biosystems, Warrington, United Kingdom). For each isolate, a confluent area of growth was sampled using a 1-µl plastic loop and transferred to a well in the MicroAmp plate. The plate was incubated at 95°C for 8 min in a PE 9700 thermocycler (Applied Biosystems, Warrington, United Kingdom) and then placed in a Jouan C4.12 centrifuge (Jouan Ltd., Ilkeston, United Kingdom) at 2,290 x g for 5 min. The resultant supernatant was used for TaqMan Probe analysis. DNA template preparation for sequencing analysis was carried out using the DNA Template Preparation Kit (14).
MIC determination. MICs were determined for erythromycin, clarithromycin, azithromycin, clindamycin, and tetracycline using the Clinical and Laboratory Standards Institute guidelines for broth microdilution methods (5).
High-throughput screening for the macrolide efflux mechanism mef. A plus/minus assay for the characterization of mef was performed using the ABI PRISM 7000 sequence detection system with the manufacturer's standard assay parameters and conditions (Applied Biosystems). The primers (mefEF2 and mefER2) and probe (mefEP2) used, which were designed using the mef(E) sequence (NCBI accession number U83667) and the Primer Express software package (Applied Biosystems), are shown in Table 1.
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TABLE 1. PCR and sequencing primers and probes used for characterization of the mef gene
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Sequencing of PCR products. PCR products were prepared for cycle sequencing using shrimp alkaline phosphatase (SAP) (GE Healthcare, Little Chalfont, United Kingdom) and exonuclease I (GE Healthcare) treatment. Briefly, 5 µl of each PCR product was added to 5 µl of reaction mixture (1 U SAP and 1 U exonuclease I in DNase/RNase-free H2O) and incubated at 37°C for 60 min, followed by 75°C for 15 min to inactivate the enzymes. Each sample was then diluted 1 in 5 by adding 40 µl of DNase/RNase-free H2O. The primers used for sequencing were as previously published (6, 15, 16). A further sequencing primer, listed in Table 1 (mef 5 R), was used in the original amplification, while primers mef 8 F and mef 6 R were used as sequencing primers for the mef 8 F and mef 6 R PCR amplification. Each diluted SAP/exonuclease I nuclease-treated product (5 µl) was added to 15 µl of a reaction mixture containing 1 µl Ready Reaction Mix (Applied Biosystems, Warrington, United Kingdom), 4 µl of 5x sequencing buffer (Applied Biosystems), 9.5 µl of RNase- and DNase-free sterile distilled H2O (Sigma, Poole, United Kingdom), and 3.2 pmol of each target-specific forward and reverse primer. The cycling parameters were 25 cycles of 96°C for 10 s, 50°C for 5 s, and 60°C for 4 min.
Mosaic structure characterization. The method used to emphasize the mosaic structure of mef was similar to a previously published method (12).
MLST. Multilocus sequence typing (MLST) was performed as previously described (8). Sequence types were determined using the MLST database (http://www.mlst.net).
All sequencing was performed on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems). Sequence analysis was performed using the DNAStar analysis program (DNAStar, Madison, WI).
emm typing. Total DNA was prepared by a Chelex-based procedure using the InstaGene Matrix (Bio-Rad Laboratories). Primers and PCR conditions for the amplification of the emm gene were according to the Centers for Disease Control and Prevention protocol (2). Distinct reference emm types (designated subtype 0) share less than 92% sequence identity over the first 90 bases encoding the deduced processed M protein. New subtypes of known types are dictated by any base change observed within the 150 bases predicted to encode the processed N terminus of the M protein. New types and subtypes are assigned by the curator of the Centers for Disease Control and Prevention streptococcal M protein gene database as described previously after inspection of the sequence data (http://www.cdc.gov/ncidod/biotech/strep/assigning.htm).
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mef sequencing results. The 54 isolates that tested negative for mef(A) with the TaqMan plus/minus assay were confirmed as negative for mef(A) by sequencing of the mef gene. Of these 54 isolates, 21 were considered to be mef(E) positive. Twelve isolates were 100% identical to the mef(E) gene sequenced in S. pneumoniae (Table 2); one isolate (GenBank accession number EU870851) was 100.0% identical to mef(E) except for a 1,218-bp insertion at position 456 corresponding to an insertion sequence (IS) 96% identical to the previously published ISSdy1 of S. dysgalactiae (GenBank accession no. AJ250837) and belonging to the IS3 family; six isolates were 99.9% homologous to mef(E), with one of the six having a stop codon at amino acid position 133 (GenBank accession number EU870853); one isolate (GenBank accession number EU870854) was 98.9% homologous to mef(E), with amino acid deletions at amino acid positions 233 to 235 (FVYdel); and one isolate was 97.8% homologous to mef(E). Five isolates (0.02%) were 97.5% identical to mef(I) at the nucleotide level (GenBank accession number EU870852). These isolates' mef(I) sequences had a single-nucleotide polymorphism (SNP) in the stop codon of the mef gene, resulting in a longer open reading frame by 9 bases. One isolate (MB56Spyo029) showed the greatest homology to mef(E), but its identity was only 96.0% (GenBank accession number EU870855). This novel mef sequence had the same SNP in the stop codon as mef(I), resulting in an open reading frame longer by 9 bases.
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TABLE 2. Numbers of isolates with a specific mef subclass and their percent identity
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FIG. 1. Diagrammatic representation of the mosaic nature of mef. The numbers represent nucleotide positions in the mef gene. Nucleotide positions 1 to 569, 1100 to 1150, and 1152 to 1218 are identical to mef(A). Nucleotide positions 570 to 617, 619 to 1051, and 1053 to 1099 are identical to mef(E). Nucleotides at positions 618 and 1052 in the mosaic variant are the same as the nucleotides present in mef(A). The nucleotide at position 1151 is identical to that in mef(E).
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FIG. 2. MLST-based dendrogram of the genetic relationships among 54 S. pyogenes isolates. The genetic distances between the strains are indicated. Strain names have been shortened, with * representing MB56Spyo. Therefore, *003 is MB56Spyo003. The percentage of nucleotides identical to the most similar mef subclass; distinguishing features, e.g., stop codon, deletion (del), or insertion (ins); the emm type; and the ST/CC are indicated.
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MIC results. The MIC50, MIC90, and MIC ranges are shown in Table 3. Isolates containing mef(E) had an erythromycin MIC50 of 8 µg/ml, 1 dilution lower than that of isolates containing mef(A) (16 µg/ml) but the same as the MIC50 of the mosaic variant of mef (8 µg/ml). The tetracycline MIC50 values for mef(E), mef(A), and the mosaic variant were 32 µg/ml, 0.25 µg/ml, and 32 µg/ml, respectively.
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TABLE 3. Distribution of MIC50, MIC90, and MIC ranges between mef(E), mef(A), and the mosaic variant
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It has also been shown that mef(I) is present in S. pyogenes, which to our knowledge has not been reported before. In this project, it has been possible to demonstrate a further mef that shows variation from all of the previously reported mef subclasses, but before adding to an already confused nomenclature of the mef gene, it is important to determine which transposons this and the previously reported mef genes are associated with in order to reduce the number of mef subclasses.
The presence of a mosaic variant of mef in S. pyogenes means that it is not possible to design a probe to distinguish the subclasses of mef. A probe is able to target only a small portion of the whole mef gene, and with the kind of variation found in S. pyogenes, this can lead to misclassification. Interestingly, the organisms containing the mosaic mef variant are from one clonal complex whose predicted founder was ST39 and were all isolated from regions within the Far East. In contrast, isolates containing mef(E) were from seven unrelated STs and emm types, although the majority belonged to ST36 and emm type 12.0. The isolate showing low identity to mef(E) (MB56Spyo001) was ST317, which was a new ST for S. pyogenes, while the isolate that contained the novel subclass of mef was a singleton in the MLST database.
S. pyogenes containing the mef(A) gene had erythromycin MIC50 values greater than that of S. pyogenes that was found to contain mef(E). This reflects the scenario found in S. pneumoniae, where isolates with mef(A) have higher median macrolide MICs than those with mef(E) (1). Macr phenotype M and tetracycline resistance in S. pneumoniae have been characterized by the mef(E)- and tet(M)-containing element Tn2009, which consists of a Tn916-like element with the mega element inserted into it (7). In S. pyogenes, the Macr phenotype M and tetracycline resistance have been characterized by an element containing mef(A) and tet(O), where mef(A) is present on a Tn1207.1-like transposon inserted into unique elements containing tet(O) (3). The isolates found to contain the mosaic variant of mef also contained tet(O) (J. Blackman Northwood, L. R. Cossins and D. J. Farrell, unpublished data), suggesting that the mosaic mef variant is present on an element similar to that of mef(A)-tet(O) previously described in S. pyogenes.
The characterization of mef(E) in S. pyogenes has highlighted the need to distinguish mef(A), mef(E), and the variations of mef separately. The macrolide MICs between mef(A) and mef(E), shown here and in other studies, vary (1).
Therefore, the subclasses of mef would be better described by the genetic element they are present on, with mef(A) and the mosaic variant being present on Tn1207.1-like transposons (3), mef(E) being present on mega (6), and mef(I) being present on the IQ element (11). With respect to the novel mef subclass found in this study, it will be necessary to determine the transposable element it is associated with before adding a further subclass to mef nomenclature.
We acknowledge our colleagues within the molecular biology department at Quotient Bioresearch (formerly GR Micro Ltd.).
Published ahead of print on 2 March 2009. ![]()
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