Staphylococcal cassette chromosome mec (SCCmec) typing of methicillin-resistant Staphylococcus aureus strains isolated in 11 Asian countries: a proposal for a new nomenclature for SCCmec elements

Abstract

A description of staphylococcal cassette chromosome mec (SCCmec) elements carried by 615 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 11 Asian countries is reported, and a novel nomenclatural system based on their structures is proposed. The 615 strains were classified as type 3A (370 strains), type 2A (207 strains), type 2B (32 strains), type 1B (1 strain), and nontypeable (5 strains). The previously reported type III SCCmec (DDBJ/EMBL/GenBank accession no. AB037671) carried by the MRSA strain 85/2082 was ascertained to be composed of two SCC elements, type 3A SCCmec and SCCmercury. PCR analysis indicated that 310 of 370 type 3A SCCmec strains carried both SCC elements. These strains were prevalent in eight countries: Thailand, Sri Lanka, Indonesia, Vietnam, Philippines, Saudi Arabia, India, and Singapore. The remaining 60 type 3A SCCmec strains differed with respect to the left extremity polymorphism or to the presence of ccrC. Among these, two were identified as carrying only type 3A SCCmec elements, but their left extremities differed. Type 2A SCCmec strains predominated in Korea and Japan, although the frequency of the presence of ant(4')-1 gene downstream of mecA varied (53% for Korean strains; 93% for Japanese strains). Various SCCmec elements were identified in the tested strains, and limited numbers were identified by their multilocus sequence typing genotypes. These data suggest that numerous MRSA clones are disseminated in Asian hospitals, and these consist of minor clones that are presumed to have arisen locally and major clones that are presumed to have been introduced from other countries.

FIG. 1.

Structural comparison of SCCmec elements. The structures of SCCmec elements are based on the nucleotide sequences deposited in the DDBJ/EMBL/GenBank databases under accession nos. AB033763 (type 1B SCCmec), D86934 (type 2A.1 SCCmec), AB127982 (type 2A.2) AB037671 (type 3A SCCmec), AB063172 (type 2B.1 SCCmec), AB063173 (type 2B.2 SCCmec), AB096217 (type 2B.3 SCCmec), and AB121219 (type 5C). The SCCmec element is composed of two essential gene complexes, the ccr gene complex (blue-green) and the mec gene complex (peach). The ccr gene complex consists of ccr genes that are responsible for the mobility of SCCmec and surrounding ORFs. The mec gene complex is responsible for methicillin-cephem resistance. Other areas (light gray) of SCCmec are nonessential and are divided into three regions, J1 to J3. Various drug resistance genes are found within the J2 and J3 regions of some SCCmec elements. Some ORFs specific for each type are found within the J1 region, such as pls in type I SCCmec and the kdp operon in type II SCCmec. Direct-repeat-containing integration site sequences of SCCmec elements are indicated by red arrowheads. The locations of primer sets (A to H) used for the multiplex PCR method developed by Oliveira and Lencastre (31) are indicated by red arrows. The locations of primer sets used for the identification of the J1 region (J) of type 2A and type 2B SCCmec element used in this study are indicated by red bars.

FIG. 2.

Identification of small type 3A SCCmec elements. The structures of three type 3A SCCmec elements and characteristic nucleotides at both extremities are illustrated. (A) The structure of the type 3A SCCmec element and of the SCCmercury element (formerly called type III SCCmec) is based on the nucleotide sequences deposited in DDBJ/EMBL/GenBank databases under accession no. AB037671. (B) The structure of the type 3A SCCmec elements (3A.1.1) of strain JCSC290 is derived by PCR. (C) The structure of the type 3A SCCmec elements of strain JCSC1716 (3A.1.4) is derived by PCR. Black arrowheads indicate the locations of primers used for detecting the precise excision of SCCmec or SCCmercury and for amplification of the entire region containing the two type 3A SCCmec elements carried by JCSC290 and JCSC1716. The nucleotide sequences of the primers are listed in Table 1. The nucleotide sequences of both extremities of SCCmercury and SCCmec elements are illustrated. Red arrowheads indicate directly repeated sequences that constitute the integration site of SCCmec (ISS), and their nucleotide sequences are underlined.