Volume 5, Number 2—April 1999
emm Typing and Validation of Provisional M Types for Group A Streptococci1
This report discusses the following issues related to typing of group A streptococci (GAS): The development and use of the 5' emm variable region sequencing (emm typing) in relation to the existing serologic typing system; the designation of emm types in relation to M types; a system for validation of new emm types; criteria for validation of provisional M types to new M-types; a list of reference type cultures for each of the M-type or emm-type strains of GAS; the results of the first culture exchange program for a quality control testing system among the national and World Health Organization collaborating centers for streptococci; and dissemination of new approaches to typing of GAS to the international streptococcal community.
The Lancefield M-typing system, a typical serologic system based on antigen-antibody reactions, is dependent on the preparation of type-specific antisera and extraction of a protein identified as M protein on the surface of group A streptococci (GAS) (1). The antisera against the M-protein antigens are produced with whole-cell streptococcal vaccines used to immunize rabbits. Acceptable antisera contain specific-precipitin antibodies and type-specific antibodies that must enhance the phagocytosis of the strain used to immunize the rabbit (2,3). The precipitin antibodies are made specific by absorption of the serum with streptococcal cells to remove the carbohydrate group antibodies and any cross-reactive precipitin antibody to heterologous M-type strains. Each rabbit antiserum is tested for reaction with antigens of all known M types.
Approximately half of GAS strains produce an apoproteinase, an enzyme that causes mammalian serum to increase in opacity. This reaction is called the serum opacity factor reaction, and the responsible enzyme is referred to as opacity factor (OF). The OF enzymes are OF type-specific because each M type that produces OF can induce type-specific OF antibodies that can be used in OF inhibition tests (3,4). Preparation of the OF antisera and specific details of the OF tests are described elsewhere (3,4). Some laboratories have used OF typing to predict M types in epidemiologic investigations. Even though it is not uniformly agreed that OF typing antisera results should be reported as M or provisional M-typing results, anti-OF antisera in many situations predict the M type in a type-specific manner. For reporting purposes, if cultures are identified with M- or OF-typing antisera, they should be identified as M type or OF type.
Reference strains used to prepare the M antisera (several of which were originally described by Griffith in 1935) were historically obtained from the Lancefield collection, Rockefeller University, New York; however more recently, reference strains have been available from other reference laboratories. M-types 1 through 51 were designated in the laboratory of Dr. Rebecca Lancefield between 1928 and 1945. M-types 52 through 81 were submitted by various investigators to reference laboratories in Atlanta, London, New York, and Prague between 1965 and 1976 for confirmation. Some laboratories believe that certain strains in the Lancefield collection do not adequately express M protein and are unsuitable for the production of M-type antiserum. Preparing M-type antiserum or a typing system accurately related to the Lancefield system requires documented reference strains from one of the internationally recognized reference laboratories.2
In the Lancefield typing system, strains representing types 7, 16, 20, and 21 (originally described as Griffith) are not GAS but belong to groups C and G. M-type 10 is the same serotype as M12, M-type 24 is the same as M45, and M-type 35 is the same as M49; thus, designations of serotypes 7, 10, 16, 20, 21, 35, and 45 are not included in the Lancefield M-typing system 1 to 81 for GAS.
The emm gene of S. pyogenes is the gene that encodes the M protein. The M protein, responsible for the bacterium's capacity to resist phagocytosis, is a major virulence factor in GAS. The 5' ends of emm genes are highly heterogeneous and encode for the serotype specificity used for the M-typing system developed by Dr. Lancefield in 1928 (1). Producing type-specific M-typing antisera is difficult and specialized; no attempt has ever been made to produce them commercially, and only a few international reference laboratories prepare them. The resurgence of rheumatic fever cases in the United States and the emergence of severe infections (streptococcal toxic shock and necrotizing fasciitis) caused by GAS in the 1980s and 1990s indicated the need to reassess typing strategies for GAS. Since production of M-type precipitating antisera is very expensive and labor-intensive, the potential usefulness of a nonserologic typing system for GAS sequencing the 5' end of the M protein (emm) gene toward a molecular-based typing system was examined.
emm Typing System for GAS
Before an emm genotype-based typing scheme was developed for GAS, the nucleotide sequence at the 5' ends of emm genes had been reported for many strains representing M-types 1-81 and several provisional M types (PT) (5,6). However, it was not always evident that true reference strains had been used. The knowledge gained from these studies provided the impetus for exploring the feasibility of an emm-based genotyping system. Subsequent studies based on sequencing the 5' emm genes from GAS reference strains and clinical culture specimens have now been published (7,8). In all studies involving emm sequence typing, 160 to 660 bases were sequenced from the 5' terminal end of the emm gene. The methods of emm sequencing and emm gene amplicon profiling restriction pattern techniques have been described (7,8). Two isolates are regarded as sharing the same emm sequence type if they are > 95% identical over their 5' end 160 nucleotides (includes approximately 50 bp of the moderately conserved leader peptide-coding region), allowing for one frame shift or in-frame insertion/deletion of no more than seven codons (8). The results of emm gene sequencing of Dr. Lancefield's reference strains types 1 to 51 and reference strains of M-types 52 to 81, submitted to the Centers for Disease Control and Prevention (CDC) Streptococcus Reference Laboratory as potential new M types from 1967 to 1976 by various international investigators, are summarized below.
The 5' end emm sequences of the following CDC M-type reference strains matched the following sequences in GenBank that were submitted by other investigators: Types 1, 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 36, 37, 39, 41, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 72, 73, 74, 75, 76, 77, 78, 80, 81. The accession numbers for these and many other emm sequences deposited in GenBank are listed in references 5-8 and at http://www.cdc.gov/ncidod/biotech/infotech_hp.html.
The 5' emm sequences from the CDC reference strains of GAS for the following M types were submitted to GenBank: M-types 13 (AF025950), 32 (L47325), 34 (L47324), 38/40 (L46817), 42 (L46799), 67 (AF025949), 68 (AF025948), 69 (AF035838), 70 (AF035838), 71 (L46652). The 5' emm sequences that were different from those submitted to GenBank by previous investigators (6) are M-types 13, 67, 68, and 79. For M-type 13, the emm sequence in GenBank was not from a recognized Lancefield typing strain; emm sequence AF025950 should be considered the emm sequence for Lancefield M-type 13. For M-types 67 and 68, the emm sequences in GenBank did not match those from CDC. The reasons for this are unknown; however, emm sequence AF025949 (M-type 67) and emm sequence AF025948 (M-type 68) were obtained from the reference strains submitted to CDC by the investigators who originally described these M types. For M-type 79, the emm sequence obtained by the CDC investigators matched the emm sequence in GenBank labeled M-type 80. Personal communication with the investigators who submitted the emm sequences for M-types 79 and 80 indicated a transcription error during submission of the sequences. Sequence U12004 is the correct sequence for M-type 79. The emm sequences from the CDC reference strains representing these four M types were confirmed by an independent laboratory.
CDC has additional data on emm typing of more than 1,500 GAS isolates from population-based studies, as well as random cultures from the United States and several other countries. Nearly 100% of the cultures could be genotyped by the emm typing system. In addition to determining the emm types of reference strains of M-types 1 to 81, several provisional type strains as well as new sequence type strains were typed by the emm typing procedure. Only one of more than 1,500 GAS isolates could not be emm typed by current methods. The emm sequence type of clinical isolates representing 35 distinct serotypes match the emm sequence type of the corresponding reference strain—included in this set of analyses are clinical isolates that underwent M or OF serotyping at one of the internationally recognized reference laboratories or elsewhere (8;9; B. Beall and D. Bessen, unpub. data).
The historical correlations between T type, OF reaction, and M type are largely unchanged when emm sequence type is substituted for M type (3,4,7,8). Because this observation is based upon the analysis of >3,000 clinical isolates, the T type and OF reactions together constitute an invaluable second-tier method for further confirmation of the grouping of closely related isolates, as well as for resolution of unrelated sets of organisms (R. Beall and R. Facklam, unpub. data).
When comparing a phenotypic-based typing scheme to a genotypic-based scheme, complete concordancy is not expected. Although for most types the M serotype is paired with a unique emm sequence type, there are several discrepancies. In five well-documented instances, 5' end emm sequences are >95% identical for two distinct M serotypes: M-types 27L and 77, 38 and 40, 44 and 61, 50 and 62, and 65 and 69 (10). The molecular basis for a lack of concordancy can differ for each unique M-type/emm-type pair. A few critical nucleotide substitutions at the 5' emm region could result in new, dominant antigenic epitopes that lead to the generation of a distinct serologic type. Alternatively, emm genes can occasionally undergo horizontal exchange and move onto a new genetic background, as appears to be the case for emm44 and emm61 (6); in this instance, additional dominant, polymorphic antigens may exist that can also be detected by M-typing sera. For the five examples cited above, introduction of a second typing scheme (T-agglutination and OF reaction) has proven useful in distinguishing between pairs displaying identical emm sequence types, but distinct M serotypes.
The discriminatory power of the genotypic emm sequence-typing scheme approximates that of the phenotypic M-serotyping scheme. For most M serotypes, there is a one-for-one relationship with a unique emm sequence type. The selection of 95% sequence identity as the cutoff value for defining the emm sequence type is based on empirical measures that best match the level of resolution achieved by M serotyping. In several examples, the emm sequence of one emm-type/M-type pair displays a relatively high level of sequence identity (but <95%) to a second, unique emm-type/M-type pair. For example, the emm3 and emm31 sequences share 91.3% identity over their first 160 bases; emm2 and emm73 are 89% identical over their first 160 bases of 5' end sequence, and this similarity is increased to 92.3% identity over their first 326 5' bases. Conceivably, certain genetic changes, such as a single bp insertion in the emm hypervariable region followed by a single bp deletion much farther downstream, could alter the reading frame of the gene and hence the antigenic structure and serotype of the emm gene product; however, this kind of variant has rarely been encountered in CDC surveys. Other genetic changes, such as synonymous substitutions, have no effect on phenotype. In some instances a single deletion or insertion of seven or fewer codons within the hypervariable 5' end 160 bp had no effect on the predicted M serotype (B. Beall, unpub. data). Therefore, an emm gene with less than 95% sequence identity to other emm genes may confer a new M serotype specificity. Thus, two isolates are regarded as sharing the same emm sequence type if they are >95% identical over their first 160 nucleotides, allowing for one frame shift or in-frame insertion/deletion of no more than seven codons (8). The 95% identity cutoff is not expected to match perfectly what can be achieved by serologic methods.
Most of the GAS isolates that are deemed nontypable by serologic methods can be genotyped through emm sequence determination. Furthermore, the M serotype does not always match the emm sequence-type (9,11). However, among the hundreds of strains analyzed by the streptococcal reference laboratory at CDC no discrepancies were observed between M serotype and emm sequence type. The full extent of putative M-serotype/emm sequence-type discordancies is not known, and the explanations for such a lack of congruency are numerous. A more complete understanding of the basis for discrepancies will be forthcoming as the emm sequence-typing method becomes more widely implemented.
The emm-typing system is a useful and reliable epidemiologic tool for subdividing GAS. Because it is independent of emm gene expression and can often discriminate between biologically distinct isolates that may be only weakly antigenic or nontypeable, emm sequence typing has the potential to classify isolates that have been difficult to type by serologic methods.
Designation of M, Provisional M, and emm Sequence Types
GAS strains fall into three categories: Validated M types, provisional M types, and emm sequence types. If a laboratory has prepared antiserum to an unknown strain and the serum has type-specific precipitating antibodies, as well as bactericidal antibodies directed to that strain, verified by one of the six original reference laboratories, an M-type designation can be assigned to that strain. If two laboratories (at least one being one of the six reference laboratories) produces type-specific precipitating and bactericidal antiserum to the strain, the strain also qualifies as a new M type.
When a laboratory has prepared antiserum as described above to an unknown strain but the specificity of this antiserum has not yet been confirmed by a second reference laboratory, that strain is designated a provisional type. The requirements for conventional validation of new M types will be described elsewhere. A third category are sequence types or emm types, which are strains typed by sequencing the emm gene. If cultures are identified by emm sequencing, they should be reported as emm type.
Validation Procedures and Nomenclature of New emm Sequence Type Strains
Published emm sequences from studies conducted in New Zealand and Australia included several new emm sequences included in GenBank (12,13). In addition, data from the CDC studies (B. Beall and R. Facklam, http://www.cdc.gov/ncidod/biotech/infotech_hp.html) indicated that more than 30 unknown emm sequences were identified among the 1,500 isolates of GAS that had been emm sequenced. A working group of representatives of each of the six international reference centers in Canada, New Zealand, Czech Republic, United Kingdom, and United States, was charged with establishing a definitive protocol both for submission of new emm sequences and for subsequent validation of new emm types. As an interim measure, unique 5' end emm sequences proposed as new emm types must be confirmed by a second laboratory; at least one of the two laboratories should be the streptococcal reference laboratory at CDC. If the uniqueness of the emm sequence can be confirmed by the second laboratory, the original investigator or one of the confirming laboratories will submit the findings to the Working Group, which will determine whether the strain should be assigned a new emm type number (e.g., emm94). In addition to sequence uniqueness, additional factors may be considered by the working group when making this decision; for example, previous requirements for assigning regular M- and provisional M-type numbers to strains were restricted to strains of particular clinical significance or to those occurring in a population "with significant frequency." Another remaining unresolved issue is whether or not all new emm reference strains should actively express M protein. A lack of surface expression of this emm gene product will preclude any possibility for correlation of emm type with classic serologic type or subsequent evaluation of biological significance. The relationship of emm sequence to biological function needs to be further explored.
CDC has validated six emm sequences submitted to GenBank by Australian investigators (12-14) and one emm sequence from a strain submitted to CDC by an investigator in the United States (15); these sequences should all be considered for official status as new emm types. Four additional isolates were examined at the CDC laboratory for which emm sequences had been submitted to GenBank (12-14). Strains STBSB75, ST1293, ST87/156, and STNS27 were shown to have the same emm types as M-type 70, M-type 76, PT2110, and PT5757, respectively. Therefore, these four emm sequences should not be accepted as new emm types, and their sequences should be reidentified in GenBank.
CDC has identified 10 new emm types from population-based studies of GAS invasive disease (7,8, unpub. data). In addition, eight new emm sequences from Brazil, six from Malaysia, three from Papua New Guinea, three from India, two from Ethiopia, two from Gambia, and one each from New Zealand and Chile have been confirmed by a second laboratory for emm sequence uniqueness, for 36 potentially new emm types.
List of Reference Strains
The WHO Collaborating Laboratory for Reference and Research on Streptococci in Prague has prepared a database of the reference type strains to be used for research and antiserum production from information provided by the six international Reference Centers in Canada, New Zealand, Czech Republic, United Kingdom, and United States. Although all the reference strains on the list at one time had demonstrated survival in the in vitro bactericidal test (presumably reflecting functional M protein), the reference strains should be retested for survival in the bactericidal test before use in research. Dr. Lancefield's strains types 1 to 50 are listed at http://www.rockefeller.edu/vaf/
Because listing of type strains may be slightly different for each culture collection, when cultures are obtained, the strains should be properly identified. The strains for reference types 1 to 50 should be traced to the Lancefield collection, from which the M-typing system was derived. In the past, if a reference strain lost the capacity to express M protein on the bacterial cell surface, that strain was passaged in vivo and selected for the increased presence of M protein; therefore, many derivatives of the original reference cultures are in use by the reference laboratories, and none are known to have undergone change in their emm gene nucleotide sequence. The American Type Culture Collection (ATCC) has Lancefield's strains 1 to 50, the UK National Collection of Type Cultures has types 1 to 81, as well as the provisional types, and the Czech Culture Collection in Prague also has types 1 to 81 on deposit. Reference cultures 51 to 81 have been deposited in the ATCC by the CDC investigators who will also deposit the provisional type strains shortly. Plans are to continue the deposition of cultures of new emm types as they are confirmed.
Additionally, the CDC Streptococcus Laboratory has established an emm-type database at http://www.cdc.gov/ncidod/biotech/infotech_hp.html for use as a sequence comparison tool and additional documentation of all of the verified M and emm types. The database contains detailed information on the CDC method of emm typing and provides additional background on each reference strain and most known emm sequence types. Sequence comparisons can be done by using BLAST (Basic Local Alignment Search Tool). The data are prereviewed for errors and discrepancies, and all newly deposited emm-types are first verified directly by the CDC reference laboratory. At this time, until a complete validation protocol is established, investigators who discover new emm sequence types should submit their isolates to the CDC Streptococcus Laboratory to confirm uniqueness. As a first step, investigators should search the CDC database for emm sequences; Genbank can be used as a second step, since it is always possible that neither database will necessarily have all known emm sequences of GAS at any given time. Furthermore, the CDC database will include the accepted emm type designation for those types, whereas a possible incorrect emm sequence may have been submitted to GenBank by an investigator.
Validation of Provisional M Types to New M and emm Types
The Table lists the provisional M-type strains and the status of validation. Collaborative investigations involving the six reference laboratories included several other provisional M-type strains and has confirmed the following: PT179 fulfills all the phenotypic criteria for an M type; however, only anti-OF serum has been prepared. Therefore, the status of this strain as a potential new M type remains on hold until further supporting data can be provided. PT4854, Colindale Laboratory, United Kingdom (UK), had a closely matching emm type as M-type 43; this finding correlated to serologic tests at CDC and UK laboratories as M-type 43 that demonstrate that both strains reacted with M43 typing antiserum. PT3800, Prague, Czech Republic (CZ), has the same emm type as M-type 65, which correlated to serologic tests performed at the National Streptococcus Laboratory in Edmonton, Canada, showing that both strains reacted with M65 typing antiserum. PTYE327 (CZ) has the same emm type as PT2841(UK), which correlates to serologic tests performed in both the Colindale and Prague laboratories. PT1437, Porirua Laboratory, New Zealand (NZ), has the same emm type as PT4245 (UK), which correlates to serologic tests performed in both the UK and NZ laboratories. ST2974.95 (CDC) has the same emm type as PT5118 (NZ). ST2974.95 was shown to be PT5118 in serologic tests performed in the Porirua Laboratory. In summary, PT4854, PT3800, PTYE327, PT1437, and ST2974.95 should be identified as emm43 (M43), emm65 (M65), emm87 (M87), emm89 (M89), and emm92, (M92) respectively. The sources of most provisional types were first documented in 1985 (16).
The following emm types were isolated from patients with severe invasive disease in the United States; emm82, emm83, emm86, emm87, emm88, emm89, and emm92. These isolates comprised 12.7% of all isolates identified during these studies. Types emm82, emm85, emm87, and emm89 were associated with epidemic investigations in the United States. Many of these new emm types were also identified from other countries, including Argentina, Brazil, Bulgaria, Chile, Colombia, Denmark, India, Korea, Malaysia, New Guinea, and Poland. Other reference laboratories have reported these new M types (by using provisional type identifiers) in a variety of infections, including rheumatic fever and acute glomerulonephritis (17,18).
An External Quality Assurance Typing Program among International Reference Laboratories
At the request of the World Health Organization (19), a quality assurance program on GAS typing has been established by the Central Public Health Laboratory, London, United Kingdom. Ten GAS isolates were examined by six different laboratories, and the results of the first distribution showed a very good correlation between laboratories. Emm typing by one laboratory correlated very well with M typing by the other five laboratories. Only minor differences were noted among the T- and OF-typing results; no errors were found among the M-typing results. Responsibility for sending 10 cultures to the other five centers twice a year would be rotated among the six reference centers and a report of the quality assurance program will be presented at the next International Lancefield Society meeting in New Zealand in the fall of 1999.
Dr. Richard Facklam is chief of the Streptococcus Laboratory, Division of Bacterial and Mycotic Diseases Division, National Center for Infectious Diseases, CDC. His major fields of interest include improvement in laboratory procedures for the diagnosis of acute respiratory tract infections, taxonomy of streptococci and related gram-positive cocci, identification of virulence factors associated with bacterial respiratory pathogens, and development of new systems for epidemiologic study of the transmission of bacterial respiratory pathogens.
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Suggested citation: Facklam R, Beall B, Efstratiou a, Fischetti V, Johnson D, Kaplan E, et al. emm Typing and Validation of Provisional M Types for Group A Streptococci. Emerg Infect Dis [serial on the Internet]. 1999, Apr [date cited]. Available from http://wwwnc.cdc.gov/eid/article/5/2/99-0209.htm
1Information in this report was first presented at an International Workshop on Demonstration of emm Typing and Validation of Provisional M types for Group A Streptococci held at the Centers for Disease Control and Prevention, Atlanta, Georgia, August 26-28, 1997.
2Centers for Disease Control and Prevention, Atlanta, Georgia, USA; Central Public Health Laboratory, London, United Kingdom; The Rockefeller University, New York, New York, USA; University of Minnesota, Minneapolis, Minnesota, USA; National Institute of Public Health, Prague, Czech Republic, National Center for Streptococcus, Edmonton, Alberta, Canada; Communicable Disease Group, ESR, Porirua, New Zealand.