[show abstract][hide abstract] ABSTRACT: Recently, we introduced the complete genome sequence of Mycobacterium massiliense clinical isolates, Asan 50594 belonging to Type II genotype with rough colony morphology. Here, to address the issue of whether the rough colony morphotype of M. massiliense Type II genotype is genetically determined or not, we compared polymorphisms of the glycopeptidolipid (GPL) gene locus between M. massiliense Type II Asan 50594 and other rapidly growing mycobacteria (RGM) strains via analysis of genome databases.
We found deletions of 10 genes (24.8 kb), in the GPL biosynthesis related gene cluster of Asan 50594 genome, but no deletions in those of other smooth RGMs. To check the presence of deletions of GPL biosynthesis related genes in Mycobacterium abscessus - complex strains, PCRs targeting 12 different GPL genes (10 genes deleted in Asan 50594 genome as well as 2 conserved genes) were applied into 76 clinical strains of the M. abscessus complex strains [54 strains (Type I: 33, and Type II: 21) of M. massiliense and 22 strains (rough morphoype: 11 and smooth morphotype: 11) of M. abscessus]. No strains of the Type II genotype produced PCR amplicons in a total of 10 deleted GPL genes, suggesting loss of GPL biosynthesis genes in the genome of M. massiliense type II genotype strains.
Our data suggested that the rough colony morphotype of the M. massiliense Type II genotype may be acquired via deletion events at the GPL gene locus for evolutionary adaptation between the host and pathogen.
[show abstract][hide abstract] ABSTRACT: A previously undescribed, a slow growing scoto-chromogenic mycobacterial species was isolated from a patient with pulmonary infections during the hsp65 sequence based identification of Korean clinical isolates. Growth characteristics, acid fastness, and results of 16S rDNA sequencing supported the placement of this species into the genus Mycobacterium. Phenotypically, this strain was generally similar to Mycobacterium gordonae, however, of particular interest, the optimal growth temperature of strain 49061T was 25 to 30 , and it is not able to grow at 37 on 7H10 agar slant. Its 16S rRNA sequence was unique and the phylogenetic analysis based on 16S rRNA sequence (1393 bp) placed the organism into the slow growing Mycobacterium group close to Mycobacterium gordonae (99.0 % of sequence similarity). Unique MALDI-TOF MS profiles of lipids, phylogenetic analysis based on other two different gene sequences (hsp65 and rpoB) and a low DNA-DNA relatedness (46.52 ± 0.7) strongly supported the taxonomic status of this strain as a distinct species from M. gordonae. The type strain is strain 49061T (=JCM 18565T=KCTC 29126T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 09/2013; · 2.11 Impact Factor
[show abstract][hide abstract] ABSTRACT: Recently, a novel species, Mycobacterium yongonense (DSM 45126(T)), was introduced and while it is phylogenetically related to Mycobacterium intracellulare, it has a distinct RNA polymerase β-subunit gene (rpoB) sequence that is identical to that of Mycobacterium parascrofulaceum, which is a distantly related scotochromogen, which suggests the acquisition of the rpoB gene via a potential lateral gene transfer (LGT) event. The aims of this study are to prove the presence of the LGT event in the rpoB gene of the M. yongonense strains via multilocus sequence analysis (MLSA). In order to determine the potential of an LGT event in the rpoB gene of the M. yongonense, the MLSA based on full rpoB sequences (3447 or 3450 bp) and on partial sequences of five other targets [16S rRNA (1383 or 1395 bp), hsp65 (603 bp), dnaJ (192 bp), recA (1053 bp), and sodA (501 bp)] were conducted. Incongruences between the phylogenetic analysis of the full rpoB and the five other genes in a total of three M. yongonense strains [two clinical strains (MOTT-12 and MOTT-27) and one type strain (DSM 45126(T))] were observed, suggesting that rpoB gene of three M. yongonense strains may have been acquired very recently via an LGT event from M. parascrofulaceum, which is a distantly related scotochromogen.
PLoS ONE 01/2013; 8(1):e51846. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: We report the complete genome sequence of the Mycobacterium massiliense clinical strain Asan 50594, which was grouped into the M. massiliense type II genotype, isolated from a Korean patient. This genome sequence will serve as a valuable reference for understanding the disparity in virulence and epidemiological traits between strains belonging to the Mycobacterium abscessus complex.
[show abstract][hide abstract] ABSTRACT: A previously undescribed, slowly growing, non-chromogenic Mycobacterium strain (strain 299T) was isolated from the sputum sample of a patient with a symptomatic pulmonary infection. Phenotypically, strain 299T was generally similar to Mycobacterium koreense DSM 45576T and M. triviale ATCC 23292T. The 16S rRNA gene sequence of strain 299T was similar to those of M. koreense DSM 45576T (AY734996, 99.5 % similarity); however, it differed substantially from that of M. triviale ATCC 23292T (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain 299T was clustered together with M. koreense DSM 45576T and M. triviale ATCC 23292T, supported by the high bootstrapping values (99 %). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 299T represents a novel mycobacterial species, for which the name M. parakoreense sp. nov. is proposed. The type strain is the strain 299T (=DSM 45575T=KCTC 19818T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 11/2012; · 2.11 Impact Factor
[show abstract][hide abstract] ABSTRACT: Here we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-36Y, previously grouped into the INT5 genotype among the 5 genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in virulence and epidemiologic traits between M. intracellulare-related strains.
Journal of bacteriology 08/2012; 194(15):4141-2. · 3.94 Impact Factor
[show abstract][hide abstract] ABSTRACT: The population structure of Korean (150 strains) and Japanese (92 strains) Legionella pneumophila isolates along with 18 reference strains were investigated using hsp60 sequence (1647 bp) analysis. Twelve clonal subgroups (hsP-I to hsP-X and hsF-I and hsF-II) were designated on the hsp60 tree, inferred from representative sequences using the neighbor-joining method. Some of the isolates showed unique subgroups depending on the source of isolates, including hsP-I, hsF-I, and hsF-II from cooling tower water, and subgroups hsP-VIII and hsP-X from circulating hot water bath. These subgroups may be useful for epidemiological studies to chase or specify sources of infection in Korea and Japan.
Microbiology and Immunology 06/2012; 56(8):572-8. · 1.55 Impact Factor
[show abstract][hide abstract] ABSTRACT: Pyrazinamide (PZA) is an effective antitubercular drug that becomes toxic to Mycobacterium tuberculosis when converted to pyrazinoic acid by pyrazinamidase (PZase), encoded by mycobacterial pncA. A strong association was noted between the loss of PZase activity and PZA resistance. The causative organisms in extrapulmonary tuberculosis are rarely cultured and isolated. To detect pncA mutations in specimens from extrapulmonary tuberculosis as confirmative diagnosis of mycobacterial infection and alternative susceptibility test to PZA.
Specimens were collected from clinically proven extrapulmonary tuberculosis. pncA was sequenced and compared with wild-type pncA.
pncA from 30 specimens from 23 donors were successfully amplified (56.6% in specimens, 59% in donors). Six mutations in pncA were detected (20.0% in amplified specimens, 26.1% in specimen donors) at nucleotide positions of 169, 248 and 419. The mutation at position 169 results in substitution of aspartic acid for histidine, a possible allelic variation of M. bovis that have intrinsic PZA resistance. The mutation at position 248 changes proline into arginine and that at position 419, arginine into histidine.
DNA-based diagnosis using pncA may be simultaneously useful for the early diagnosis of mycobacterial infection and the rapid susceptibility to PZA in extrapulmonary tuberculosis. A potential implication of pncA allelic variation at 169 might be suggested as a rapid diagnostic test for M. bovis infection or Bacille Calmette-Guérin (BCG) reactivation.
Tuberculosis and respiratory diseases. 06/2012; 72(6):475-80.
[show abstract][hide abstract] ABSTRACT: Here, we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-64, previously grouped into the INT1 genotype among five genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in the virulence and epidemiologic traits among M. intracellulare genotypes.
Journal of bacteriology 06/2012; 194(12):3268. · 3.94 Impact Factor
[show abstract][hide abstract] ABSTRACT: Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC 13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of the disparity between MAC members.
Journal of bacteriology 05/2012; 194(10):2750. · 3.94 Impact Factor
[show abstract][hide abstract] ABSTRACT: Here, we report the first complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-02, which was previously grouped in the INT2 genotype of M. intracellulare. This genome sequence will serve as a valuable reference for improving the understanding of the disparity in the virulence and epidemiologic traits between M. intracellulare genotypes.
Journal of bacteriology 05/2012; 194(10):2771. · 3.94 Impact Factor
[show abstract][hide abstract] ABSTRACT: A previously unknown, slow growing nonchromogenic mycobacterial species was isolated from a patient with pulmonary symptoms. Phenotypically, the strain 05-1390T was similar to Mycobacterium intracellulare ATCC 13950T. The 16S rRNA gene sequence (1385 bp) of this strain showed a high degree of similarity with the M. intracellulare related species, Mycobacterium marseillense strain 5351974T (100 %), M. intracellulare ATCC 13950T (99.8 %) and Mycobacterium chimaera DSM 44623T (99.9 %). Phylogenetic analysis based on the internal transcribed sequences (ITS1) and the hsp65 gene indicated that 05-1390T is closely related to M. intracellulare ATCC 13950T, but that it is of a distinct phylogenetic entity. Of particular interest, an analysis based on the rpoB gene (701 bp) showed that it is closely related to Mycobacterium parascrofulaceum ATCC BAA-614T (99.4 %), a scotochromogenic strain, rather than to the M. intracellulare-related strains. Unique mycolic acid and MALDI-TOF MS profiles also supported the taxonomic status of this strain as a distinct species. These data support the conclusion that the strain represents a new mycobacterial species, for which the name Mycobacterium yongonense sp. nov. is proposed. The type strain is strain 05-1390T (= DSM 45126T = KCTC 19555T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 03/2012; · 2.11 Impact Factor
[show abstract][hide abstract] ABSTRACT: SUMMARY We conducted an epidemic investigation to discover the route of transmission and the host factors of an outbreak of post-injection abscesses. Of the 2984 patients who visited a single clinic, 77 cases were identified and 208 age- and sex-matched controls were selected for analysis. Injected medications per se were not found to be responsible, and a deviation from safe injection practice suggested the likelihood of diluent contamination. Therefore the injected medications were classified according to whether there was a need for a diluent, and two medications showed a statistically significant association, i.e. injection with pheniramine [adjusted odds ratios (aOR) 5·93, 95% confidence interval (CI) 2·97-11·87] and ribostamycin (aOR 47·95, 95% CI 11·08-207·53). However, when considered concurrently, pheniramine lost statistical significance (aOR 8·71, 95% CI 0·44-171·61) suggesting that normal saline was the causative agent of this outbreak. Epidemiological evidence strongly suggested that this post-injection outbreak was caused by saline contaminated with Mycobacterium massiliense without direct microbiological evidence.
Epidemiology and Infection 01/2012; 140(10):1880-7. · 2.87 Impact Factor
[show abstract][hide abstract] ABSTRACT: Previous studies have proved the presence of several distinct types of mutations in hepatitis B virus (HBV) infections, which are related to the progression of liver disease. However, few reports have detailed the mutation frequencies and mutation patterns in the precore/core (preC/C) region, which are based on the clinical status and HBeAg serostatus. Our aim in this study is to investigate the relationships between the preC/C mutations and clinical severity or HBeAg serostatus from patients chronically infected with HBV genotype C. A total of 70 Korean chronic patients, including 35 with hepatocellular carcinoma (HCC), participated in this study. HBV genotyping and precore/core mutations were analyzed by direct sequencing. All patients were confirmed to have genotype C infections. Mutations in the C region were distributed in a non-random manner. In particular, mutations in the MHC class II restricted region were found to be significantly related to HCC. Six (preC-W28*, C-P5H/L/T, C-E83D, C-I97F/L, C-L100I and C-Q182K/*) and seven types (preC-W28*, preC-G29D, C-D32N/H, C-E43K, C-P50A/H/Y, C-A131G/N/P and C-S181H/P) of mutations in the preC/C region were found to be related to HCC and to affect the HBeAg serostatus, respectively. In conclusion, our data indicated that HBV variants in the C region, particularly in the MHC class II restricted region, may contribute to the progress of HCC in chronic patients infected with genotype C. In addition, we found several distinct preC/C mutations in the Korean chronic cohort, which affect the clinical status of HCC and HBeAg serostatus of patients infected with genotype C.
PLoS ONE 01/2012; 7(10):e47372. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: So far, genetic diversity among strains within Mycobacterium massiliense has rarely been studied. To investigate the genetic diversity among M. massiliense, we conducted phylogenetic analysis based on hsp65 (603-bp) and rpoB (711-bp) sequences from 65 M. massiliense Korean isolates. We found that hsp65 sequence analysis could clearly differentiate them into two distinct genotypes, Type I and Type II, which were isolated from 35 (53.8%) and 30 patients (46.2%), respectively. The rpoB sequence analysis revealed a total of four genotypes (R-I to R-IV) within M. massiliense strains, three of which (R-I, R-II and R-III) correlated with hsp65 Type I, and other (R-IV), which correlated with Type II. Interestingly, genotyping by the hsp65 method agreed well with colony morphology. Despite some exceptions, Type I and II correlated with smooth and rough colonies, respectively. Also, both types were completely different from one another in terms of MALDI-TOF mass spectrometry profiles of whole lipid. In addition, we developed PCR-restriction analysis (PRA) based on the Hinf I digestion of 644-bp hsp65 PCR amplicons, which enables the two genotypes within M. massiliense to be easily and reliably separated. In conclusion, two distinct hsp65 genotypes exist within M. massiliense strains, which differ from one another in terms of both morphology and lipid profile. Furthermore, our data indicates that Type II is a novel M. massiliense genotype being herein presented for the first time. The disparity in clinical traits between these two hsp65 genotypes needs to be exploited in the future study.
PLoS ONE 01/2012; 7(6):e38420. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: A novel slow-growing, non-chromogenic mycobacterium (strain 01-305(T)) was isolated from a patient with pulmonary dysfunction. Growth characteristics, acid-fastness and the results of 16S rRNA gene sequencing supported the placement of this strain within the genus Mycobacterium. Phenotypically, strain 01-305(T) was generally similar to Mycobacterium triviale ATCC 23292(T), but some unique biochemical characteristics were observed. The 16S rRNA gene sequence of strain 01-305(T) was similar to those of M. triviale ATCC 23290 (GenBank accession no. AY734996, 99.9 % similarity) and M. triviale ATCC 23291 (AY734995, 99.9 %); however, it differed substantially from that of M. triviale ATCC 23292(T) (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain 01-305(T) in the slow-growing Mycobacterium group close to M. triviale ATCC 23290 and M. triviale ATCC 23291, but not M. triviale ATCC 23292(T). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 01-305(T) represents a novel mycobacterial species, for which the name Mycobacterium koreense sp. nov. is proposed. The type strain is 01-305(T) ( = DSM 45576(T) = KCTC 19819(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 07/2011; 62(Pt 6):1289-95. · 2.11 Impact Factor
[show abstract][hide abstract] ABSTRACT: Hepatitis B virus (HBV) e antigen (HBeAg) seroconversion during chronic HBV infection is known to play an important role in disease progression and patient response to antiviral agents. The aim of the present study was to analyze gender disparity in distribution of major hydrophilic region (MHR) variants according to HBeAg serostatus. Prevalence of MHR variants from 68 Korean patients with chronic hepatitis (31 HBeAg-positive and 37 HBeAg-negative) was examined in terms of HBeAg serostatus and sex by direct sequencing analysis of the MHR. Gender disparity was observed in the distribution of MHR variants according to HBeAg serostatus. In male patients, the prevalence of MHR variants was significantly higher in HBeAg negative patients than in HBeAg positive patients [58.8% (10/17 patients) vs. 14.3% (3/21 patients), P=0.004]. However, the same was not true in female patients [55.0% (11/20 patients) vs. 60.0% (6/10 patients), P=1.000)]. In addition, 2 mutation types (L110I and G145A) related to HBeAg serostatus were found. In conclusion, HBeAg seroconversion in male chronic patients infected with genotype C could lead to mutations of MHR, major target to host immune response, which might in turn contribute to HBV persistence and immune evasion.
Journal of Medical Virology 03/2011; 83(3):405-11. · 2.37 Impact Factor