Indexed in MEDLINE, SCI & KoreaMed
pISSN 1011-8934   eISSN 1598-6357
Open Access, Peer-reviewed, Weekly
    J Korean Med Sci. 2010 Dec;25(12):1716-1721. English.
    Published online Nov 24, 2010.
    https://doi.org/10.3346/jkms.2010.25.12.1716
    © 2010 The Korean Academy of Medical Sciences.
    Original Article

    IS6110-Restriction Fragment Length Polymorphism and Spoligotyping Analysis of Mycobacterium tuberculosis Clinical Isolates for Investigating Epidemiologic Distribution in Korea

    Go Eun Choi,1 Mi Hee Jang,1 Eun Ju Song,1 Seok Hoon Jeong,2 Jae-Seok Kim,3 Wee Gyo Lee,4 Young Uh,5 Kyoung Ho Roh,6 Hye Soo Lee,7 Jong Hee Shin,8 Nam Hee Ryoo,9 Young Ree Kim,10 Joseph Jeong,11 Jee Hee Kim,12 Sun Min Lee,1 Jongyoun Yi,1 Sang Hyun Hwang,1 Hyung Hoi Kim,1 Eun Yup Lee,1 Chulhun L. Chang,1 Moon-Bum Kim,13 and Yeong Dae Kim14,15
      • 1Department of Laboratory Medicine, School of Medicine, Pusan National University, Busan, Korea.
      • 2Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
      • 3Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea.
      • 4Department of Laboratory Medicine, Ajou University School of Medicine, Suwon, Korea.
      • 5Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea.
      • 6Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.
      • 7Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea.
      • 8Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Korea.
      • 9Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea.
      • 10Department of Laboratory Medicine, Cheju National University College of Medicine, Jeju, Korea.
      • 11Department of Laboratory Medicine, Ulsan University Hospital & Ulsan University College of Medicine, Ulsan, Korea.
      • 12Department of Emergency Medical Technology, Kangwon National University, Samcheok, Korea.
      • 13Department of Dermatology, School of Medicine, Pusan National University, Busan, Korea.
      • 14Department of Thoracic and Cardiovascular Surgery, School of Medicine, Pusan National University, Busan, Korea.
      • 15Medical Research Institute, Pusan National University, Busan, Korea.
    • Address for Correspondence: Yeong Dae Kim, M.D. Department of Thoracic and Cardiovascular Surgery, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 602-739, Korea. Tel: +82.51-240-7822, Fax: +82.51-243-9389, Email: domini@pnu.edu
    Received April 30, 2010; Accepted July 22, 2010.

    This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Abstract

    The Beijing family of Mycobacterium tuberculosis has been emerging in the world. However, there are few nationwide data of genotypic distribution in Korea. This study aimed to identify the genotypic diversity of clinical isolates of M. tuberculosis and to demonstrate the population of Beijing family in Korea. We collected 96 clinical M. tuberculosis isolates from 11 university hospitals nationwide in Korea from 2008 to 2009. We observed 24 clusters in IS6110-RFLP analysis and 19 patterns in spoligotyping. Seventy-five isolates were confirmed to be Beijing family. Two isolates of the K strain and 12 isolates of the K family strain were also found. We found that drug resistance phenotypes were more strongly associated with Beijing family than non-Beijing family (P=0.003). This study gives an overview of the distribution of genotypes of M. tuberculosis in Korea. These findings indicate that we have to pay more attention to control of M. tuberculosis strains associated with the Beijing family.

    Keywords
    Mycobacterium tuberculosis; IS6110-RFLP; Spoligotyping; Beijing Family; K Strain

    INTRODUCTION

    Tuberculosis (TB) remains a worldwide healthcare concern, being characterized as an epidemic by the World Health Organization (WHO). In 2008, there were an estimated 8.9-9.9 million incident cases of TB, 9.6-13.3 million prevalent cases, 1.1-1.7 million deaths among HIV-negative people and an additional 0.45-0.62 million deaths among HIV-positive people (1). In Korea, the prevalence of TB was estimated to be 123 per 100,000 in 2006 (2). The increasing number of drug-resistant Mycobacterium tuberculosis isolates, including multidrug-resistant M. tuberculosis (MDR-TB) creates serious problems in clinical series and whole-country cohorts (3).

    Genotyping has allowed the association of particular strain families of M. tuberculosis with demographic and transmission characteristics (4). The IS6110-based restriction fragment length polymorphism (RFLP) is the most widely applied test and currently the standard method for comparing the genetic relatedness of M. tuberculosis strains. Spoligotyping using the direct repeat locus (DR) is useful for both clinical management and molecular epidemiologic studies of M. tuberculosis (5).

    For a long time, the Beijing family which may have been endemic in China, has been emerging in other parts of the world (6). The Beijing M. tuberculosis strains have highly similar multibanded IS6110-RFLP patterns and identical spoligotyping patterns. The family is highly prevalent in East Asia (7, 8). However, there are few data on the nationwide genotypic distribution in Korea (8, 9).

    This study aimed to identify the genotypic diversity of clinical M. tuberculosis isolates and to demonstrate the prevalence of Beijing family strains in Korea using IS6110-RFLP and spoligotyping methods.

    MATERIALS AND METHODS

    Sample collection and bacterial strains

    From 2008 to 2009, we collected 96 clinical M. tuberculosis isolates from 11 university hospitals nationwide in Korea (Ajou University Hospital, Cheju National University Hospital, Chonbuk National University Hospital, Chonnam National University Hospital, Hallym University Hospital, Keimyung University Hospital, Konyang University Hospital, Pusan National University Hospital, Ulsan University Hospital, Yonsei University Severance Hospital, and Wonju Christian Hospital). The number of isolates from a given hospital was roughly proportional to the prevalence of TB in that area, as judged by the annual report on TB patient notification in Korea 2007 (10). The source patients were 58 men and 38 women TB patients with a mean age of 45 yr (range 21-78 yr). There were 82 primary TB infections, and 12 had a history of treatment. In two cases, the status was unknown because of follow-up loss. The sites of infection were not specified. Duplicated isolates from the same patient were excluded.

    DNA extraction

    Chromosomal DNA was purified by the standardized method from Löwenstein-Jensen (L-J) slant-grown colonies (11). Briefly, lysozyme (1 mg/mL) was added colony-containing tube and the mixture was incubated for 1 hr at 37℃. Next, proteinase K (10 mg/mL) and 70 µL of 10% sodium dodecyl sulfate were added, and incubation was continued for 10 min at 65℃. Then N-acetyl-N,N,N-trimethyl ammonium bromide was added, and the mixture was incubated for 10 min at 65℃. An equal volume of chloroform-isoamyl alcohol (24:1 vol/vol) was added. After centrifugation for 5 min, 0.6 volume of isopropanol was added to the supernatant liquid to precipitate the DNA. After 20 min at -20℃ and centrifugation for 15 min, the pellet was washed once with 70% ethanol, and the air-dried pellet was dissolved in 20 µL of 0.1×Tris-EDTA (TE) buffer.

    IS6110-RFLP

    All isolates were subjected to IS6110-RFLP analysis by an internationally standardized method (12). Briefly, the chromosomal DNA was restricted with PvuII for RFLP analysis. The digested DNA was separated overnight by gel electrophoresis and transferred from the gel to a positively charged nylon membrane (Hybond N1) (Amersham, Buckinghamshire, UK). After hybridization for repetitive elements with labeled DNA probes, the bound probes were detected with an enhanced chemiluminescence direct nucleic acid system (Amersham) according to the manufacturer's recommendations. The RFLP patterns were analyzed by GelComparII software (Applied Maths, Korthrijk, Belgium) (9).

    Spoligotyping

    Spoligotyping was carried out using a Combi™ chip spoligotyping kit (GeneIn, Inc., Busan, Korea) according to the manufacturer's instructions. Briefly, the DNAs of the whole DR region were amplified, and the amplified DNAs were hybridized with 43 spoligotyping probes as described (13). After the results had been converted with binary and octal code, the spoligotypes were designated as a cluster and assigned a shared international type number (SIT) according to the international database, SpolDB4 (14).

    Determination and analysis of Beijing family and K strains

    We determined Beijing family strains on the basis of several genetic characteristics. By definition, they have an IS6110 insertion A1 band in the origin of replication (corresponding to a 3.36-kb band) and show an IS6110 banding pattern similar to that of strain Beijing (copy number range 15-26) (15). They contain nine spacers from 35 to 43 in the spoligotype pattern (16). The Beijing-like family was identified by SpolDB4. K strain (Korean M. tuberculosis strain) was also identified, which was previously defined as a sublineage of the Beijing strain and has a unique ten IS6110 RFLP band pattern (17). The K family was identified by the characteristics that had eight to twelve IS6110 bands, and more than five bands were as same those of as K strains (17).

    Drug susceptibility testing

    Antibiotic susceptibility testing was performed at the Korean Institute of Tuberculosis by the proportion method using L-J medium against 11 antibiotics: isoniazid (INH), rifampin (RIF), ethambutol, streptomycin, capreomycin, kanamycin, ofloxacin, prothionamide, cycloserine, p-aminosalicylic acid, and rifabutin (18). The drug susceptibility test for pyrazinamide was determined using the pyrazinamidase assay (19).

    Statistical analysis

    Data were analyzed with SPSS 12.0 (SPSS Inc., Chicago, IL, USA). Categorical variables were compared by Fisher's exact test. Significance was defined as a P value of <0.05.

    Ethics statement

    This research was exempted from full committee review of Institutional Review Board at Pusan National University Hospital because cultured bacterial isolates were used without any identifiers linked to the subjects.

    RESULTS

    IS6110-RFLP patterns of 96 strains

    The IS6110 copy numbers ranged from 5 to 21 (mode=10) (Fig. 1). The majority of the strains (45/96, 46.9%) contained 9-11 copies. With a 60% similarity threshold, 24 clusters were observed in the dendrogram based IS6110-RFLP. A total of 86 isolates (89.6%) displayed one of 14 clusters and 10 isolates (10.4%) displayed unique patterns. Two pairs of four isolates showed identical IS6110-RFLP patterns in each pair (solid boxes on right in Fig. 1); the source patients for each pair had no epidemiologic linkage.

    Fig. 1
    Results of RFLP and spoligotyping of 96 M. tuberculosis isolates. Two solid boxes indicate that the two pairs of four isolates showed identical IS6110-RFLP patterns in each pair.

    Spoligotyping patterns of 96 strains

    Eighteen spoligotyping patterns were observed. Among the isolates, 85 (88.5%) displayed one of 7 spoligotypes and 11 (11.4%) displayed unique spoligotypes. According to the SpolDB4, 85 isolates (88.5%) were classified into nine shared international types (SITs), whereas 11 isolates were not classified. Among the nine clusters identified by SpolDB4 analysis, the SIT1 cluster contained a majority of the isolates (62/96, 64.6%). When considering all spoligotypes, the Beijing, including the SIT1 cluster, was the most prevalent (69/96, 71.9%), followed by seven (7.3%) Beijing-like spoligotypes, four (4.2%) CAS family, three (3.1%) U family, and two (2.1%) T1 family (Table 1).

    Table 1
    Results of spoligotyping

    Distribution of Beijing and K strains

    When analyzing IS6110-RFLP patterns, 83 of 96 isolates (86.5%) that contained the Beijing-specific A1 insertion band were determined to be Beijing family. However, 75 of these 86 isolates, and another isolate with no A1 band were confirmed to be Beijing family by spoligotyping (Fig. 1). These isolates each had 8 to 21 bands (mode 10). The unique IS6110-RFLP pattern of K strain was found in 2 isolates (2.1%), and 12 isolates (12.5%) closely resembled the K family strain. Of the 76 Beijing family strains, K family strains accounted for 18.4%.

    Relation between genotypes and drug resistances

    In this study, 21 isolates were resistant to at least one anti-tuberculosis drug. Nine of these were MDR-TB. Nineteen of 21 isolates resistant to at least one drug and all nine MDR-TB isolates belonged to the Beijing family, meaning there is a significantly higher rate of MDR or any drug resistance in the Beijing family (P=0.003) (Table 2). The differences in the resistance rates between K family and non-K Beijing family were not significant. Drug resistance rates in the study population were 9.4% (9/96) for MDR-TB and 21.9% (21/96) for at least one drug, including INH and RIF. For primary TB cases, the drug resistance rates were 2.4% (2/82) for MDR-TB and 15.9% (13/82) for at least one drug, including INH and RIF.

    Table 2
    Spoligotype and drug resistance in 96 M. tuberculosis clinical isolates

    DISCUSSION

    The Beijing family of M. tuberculosis strains may have been endemic in China for a long time (6) and is now emerging in other parts of the world. This family is dominant in Asian countries such as China (86%), Mongolia (50%), Japan (73%), Indonesia (34%), Thailand (44%), and Vietnam (54%) (7, 8, 20-22). It also is present in Korea. In a 1995 report, 43% of tested strains (6/14) were the Beijing family (8). In another report, 72% (99/138) were the Beijing family, which was defined by IS6110-RFLP patterns (9). The current study shows a higher rate of the Beijing family (79%), nearly same as the rates in China and Japan. In the first report from Korea (8), the selection criteria for the tested strains were not specified, and the test volume was small. In contrast, the two other studies including the current study, examined strains from several areas in Korea, and the number of tested strains was roughly proportional to the number of TB patients reported from each area. Very recently, one report claimed that nearly all the isolates in one Korean tertiary TB hospital were Beijing family (23). However, this hospital normally recruits drug-resistant or treatment failure cases from the entire country, so the strain population could be distorted. Therefore, our data appear to represent the genuine distribution of the Beijing family in Korea. Although isolates were collected from 11 university hospitals throughout the country, we did not find any association between the Beijing family and region. Also, no correlation between Beijing family and the sex or age of the patients was found. Two pairs of isolates from each of two university hospitals showed identical IS6110-RFLP patterns, but we did not find an epidemiological relation between the genotypes of the strains. That means that identical IS6110-RFLP patterns do not always indicate strains of the same origin.

    The Beijing family organisms have multiple copies of IS6110 bands (15 to 26), and therefore, differentiation between strains is not easy (24, 25). Many other characteristics have been demonstrated to identify the Beijing family by IS6110-RFLP analysis. In the current study, the A1 band in the IS6110 RFLP pattern was used to identify 83 strains presumablely as Beijing family, of which 76 were confirmed as such by spoligotyping. However, 19 Beijing reference strains suggested by Kremer et al. and at least 450 IS6110 profiles reported by the Public Health Research Institute (PHRI) TB Center database were not useful in detecting Beijing strains in this study (data not shown) (24, 26). A dendrogram of the IS6110-RFLP band pattern was diverse even within the Beijing family, showing that the 76 strains belonged to 18 clusters. Interestingly, the Beijing family strains tested in this study harbored relatively small numbers of IS6110 bands (8 to 21), indicating that the characteristics of the Beijing family isolated in Korea are different from those isolated in other countries. Mycobacterial interspersed repetitive units (MIRU)-variable number of tandem repeats (VNTR), another molecular epidemiologic tool for M. tuberculosis, was introduced to genotype M. tuberculosis isolates from Korea (4, 27). The MIRU-VNTR is highly discriminatory and easy to use, and can differentiate strains belonged to the Beijing family (4). However, it is not suitable for demonstrating the population of Beijing strains because it cannot provide any information distinguishing Beijing from non-Beijing family strains. In previous studies, the dominant M. tuberculosis strains in Korea were defined as the K strain, a sublineage of the Beijing strain (17). According to the definition, two isolates (2.1%) were identified with K strains and 12 isolates (12.5%) with the K family in the current study. These figures are slightly lower than those in the report of Park et al. (18.8%) from Korea (28). However, these data were developed with strains from one area, Gyeonggi Province; to estimate the population of the K family throughout Korea, a large-scale study using nationwide collection would be necessary.

    The effect of Beijing family strains on drug resistance is not clear (29), but the Beijing family is reported to have a higher rate of resistance (25). We also demonstrated that drug resistance was strongly associated with Beijing family strains in Korea. All MDR-TB isolates and the majority (19/21) of the isolates with at least one drug resistance belonged to the Beijing family. One recent study reported interesting data that in one Korean TB hospital, which specializes in caring for patients with drug-resistant TB, 97% of the isolates belonged to the Beijing family (23). This suggests a close connection between drug resistance and Beijing family membership. Therefore, patients found to be infected with M. tuberculosis of the Beijing family should be monitored closely for drug-taking compliance or response to therapy. Spoligotyping analysis could easily classify and be useful to detect Beijing strains. The 76 isolates of the Beijing family belonged to only five clusters according to the international spoligotype database, SpolDB4. Therefore, when considering that it is important to identify Beijing family members, spoligotyping can be performed more easily and rapidly than IS6110-RFLP analysis. Another issue regarding drug resistance is the primary or acquired resistance rate of M. tuberculosis. Bai et al. (30) reported that in 2004, the resistance rates were 2.7% for MDR and 12.8% for any one drug resistance in new TB cases and 14% for MDR and 27.7% for any one drug resistance among patients with a history of treatment in Korea. In the current study, the drug resistance rates in primary TB cases appeared 2.4% for MDR-TB and 15.9% for any one drug resistance, representing a similar result with the previous report.

    In summary, this study gives an overview of the distribution of genotypes of clinical M. tuberculosis isolates in Korea. Our data showed that the Beijing strain currently is the most prevalent. Especially, we found an association between Beijing family strains and drug resistance phenotypes. These findings indicate that we have to pay more attention to control of M. tuberculosis strains associated with the Beijing family. Our data also indicate that a poor drug treatment outcome may occur more commonly in Beijing family strains.

    Notes

    This work was supported by the Korea Research Foundation Grant funded by the Korean Government (Ministry of Education and Human Resources Development, Basic Research Promotion Fund) (KRF-2007-331-E00209).

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    MeSH Terms
    Drug Resistance, Bacterial
    Genotype
    Humans
    Microbial Sensitivity Tests
    Mycobacterium tuberculosis/classification*
    Mycobacterium tuberculosis/genetics
    Mycobacterium tuberculosis/isolation & purification
    Phenotype
    Polymorphism, Restriction Fragment Length
    Republic of Korea
    Tuberculosis/epidemiology*
    Tuberculosis/genetics
    Tuberculosis/microbiology
    Metrics
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