Paradigm for diagnosing mycobacterial disease: direct detection and differentiation of Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in clinical specimens using multiplex real-time PCR.

AIMS: Mycobacterium tuberculosis and non-tuberculous mycobacteria (NTM) are clinically different, and the rapid detection and differentiation of M. tuberculosis complex (MTBC) and NTM is crucial for patient management and infection control. Given the slow growth of most pathogenic mycobacteria, nucleic acid amplification assays are excellent tools for direct identification of mycobacteria in clinical specimens. Recently, a multiplex real-time PCR assay was developed that can directly detect 20 mycobacterial species in clinical specimens. Here, we evaluated the diagnostic performance of the assay for diagnosing mycobacterial disease under routine laboratory conditions. METHODS: A total of 3334 specimens collected from 1437 patients suspected of tuberculosis infection were subjected to acid-fast bacilli staining, conventional culture and the multiplex real-time PCR assay. To evaluate the sensitivity and specificity of the assay, the overall diagnosis of tuberculosis was defined by positive culture plus medical history, and the 2007 American Thoracic Society and Infectious Disease Society of America diagnostic criteria for NTM disease were applied. RESULTS: The sensitivity, specificity, positive predictive value and negative predictive value were 87.5%, 99.6%, 96.1% and 98.5%, respectively, for the detection of MTBC isolates and 53.3%, 99.9%, 95.2%, and 98.9%, respectively, for detecting NTM isolates. CONCLUSIONS: Thus, the assay can correctly differentiate between MTBC and NTM isolates in clinical specimens and would be a useful tool for the rapid differentiation of tuberculosis and NTM disease, despite its limited sensitivity for the diagnosis of NTM disease.

Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method.

Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic.

A challenging diagnosis: crystal-storing histiocytosis in plasma cell myeloma.

OBJECTIVES: Crystal-storing histiocytosis (CSH) is an uncommon finding in plasma cell neoplasms. CSH is thought to be an intralysosomal deposition of secreted paraproteins or immunoglobulins, which usually express κ immunoglobulin light chains that finally aggregate in crystals. Because of its rarity, CSH in bone marrow often makes diagnosis difficult. METHODS: A 57-year-old woman had IgA κ monoclonal proteinemia and monoclonal proteinuria. In the bone marrow aspirate, plasma cells were initially counted less than what would be expected, whereas histiocytes with intracellular crystals were increased. Then, we used α-naphthyl acetate esterase (ANAE) staining to distinguish between true histiocytes and plasma cells. Immunostaining for κ, CD138, CD56, and CD68 was performed on a bone marrow biopsy specimen. RESULTS: True histiocytes containing crystalline inclusions were stained strongly for ANAE, while unstained cells with intracytoplasmic crystals represented plasma cells. The biopsy specimen revealed diffuse infiltration of CD138-positive plasma cells. We also confirmed the presence of plasma cells, histiocytes, and their crystallized inclusions with the immunostaining. The patient was finally diagnosed with plasma cell myeloma. CONCLUSIONS: The diagnosis was challenging; the bone marrow findings resembled features of other histiocytic disorders. The use of immunohistochemistry enabled the diagnosis of CSH in the presence of plasma cell myeloma.

CD34 and p53 immunohistochemical stains differentiate hypocellular myelodysplastic syndrome (hMDS) from aplastic anemia and a CD34 immunohistochemical stain provides useful survival information for hMDS.

BACKGROUND: The presence of significant dysplasia in bone marrow (BM) aspirates helps to distinguish between hypocellular myelodysplastic syndrome (hMDS) and aplastic anemia (AA). Occasionally, diluted BM aspirates make it difficult to recognize dysplastic changes and can also negatively affect the detection of cytogenetic abnormalities in hMDS. We evaluated the usefulness of CD34 and p53 immunoreactivity for discriminating between hMDS and AA and for estimating survival outcomes in hMDS patients. METHODS: BM clot section (BMC) or BM biopsy (BMB) specimens were obtained from 64 hMDS/AA patients (33 with hMDS and 31 with AA) and seven controls. Immunohistochemical (IHC) staining for CD34 and p53 was performed by using the EnVision detection system (Dako, Denmark). We compared the results of IHC staining, BM findings, and chromosomal analyses, and determined overall survival outcomes. RESULTS: The number of CD34- and p53-positive BM cells was higher among the patients with hMDS than among the patients with AA (P<0.001 and P=0.001, respectively). hMDS patients with increased CD34-positive cells had significantly poorer survival outcomes compared with those with normal number of CD34-positive cells (P=0.013). CONCLUSIONS: CD34 and p53 IHC stains of BMC or BMB provide useful information for differentiating between hMDS and AA. CD34 IHC staining of BMC or BMB also provides useful information for estimating survival outcomes in hMDS patients.

Direct identification of mycobacteria from culture media using a multiplex real-time PCR assay: report on its application in a clinical laboratory in a region of high tuberculosis endemicity.

There are few commercial assays that easily and correctly identify the mycobacteria from culture in a clinical laboratory with a high workload. Thus, we developed and evaluated a scheme for the identification of mycobacteria using a multiplex real-time PCR assay and report on its application in our laboratory. The scheme consisted of 3 stepwise PCRs. Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and 3 PCRs. Over the 1.5-year study period, 1136 isolates of MTC and 618 isolates of NTM were detected, and the species of 608 (98.4%) of the 618 NTM isolates were identified. We conclude that the established scheme is a very useful diagnostic approach for the rapid and accurate identification of MTC and clinically relevant NTM in a clinical laboratory in a region where tuberculosis is endemic.

Male breast adenoid cystic carcinoma.

INTRODUCTION: Adenoid cystic carcinoma (ACC) of the breast is a rare condition, and cases in male patients are even less common. CASE: We describe a case of ACC of the breast with axillary lymph node metastasis, disseminated osteolytic bone metastasis and bone marrow involvement in a 41-year-old man. CONCLUSION: Male breast ACC is an extremely rare malignancy; there can be difficulty in obtaining a final diagnosis. We report this case because of its rarity.

Multiplex real-time PCR assay for detection of methicillin-resistant Staphylococcus aureus (MRSA) strains suitable in regions of high MRSA endemicity.

A multiplex real-time PCR assay that simultaneously detects the mecA, staphylococcal cassette chromosome (SCCmec)-open reading frame X (orfX) junction, and staphylococcal 16S rRNA genes was developed and evaluated using 444 staphylococcal strains. We demonstrated that this assay resulted in fewer false-positive results than a single-locus real-time PCR assay that amplified the SCCmec-orfX junction. This assay would be useful in a clinical laboratory in a region of high endemicity for methicillin-resistant Staphylococcus aureus (MRSA) infections.

A combination of CD15/CD10, CD64/CD33, CD16/CD13 or CD11b flow cytometric granulocyte panels is sensitive and specific for diagnosis of myelodysplastic syndrome.

Flow cytometry (FCM) is a reproducible and objective technique that may be useful in the diagnosis of myelodysplastic syndrome (MDS) by detecting abnormal immunophenotypes specific to MDS. We investigated 5 granulocyte/monocyte panels by FCM to find a sensitive and specific combination of panels in order to discriminate MDS from non-clonal hematologic disorders. Bone marrow aspirates from 35 patients with MDS and 25 patients with non-clonal hematologic disorders were studied. We performed FCM using 5 granulocyte/monocyte panels (CD15/CD10/CD45, CD64/CD33/CD45, CD16/CD13/CD45, CD16/CD11b/CD45, and CD56/CD19/CD7/CD45) to examine the positive rate in MDS and controls, and to find an optimal combination that maximizes the detection rate of MDS. In MDS, the number of abnormal immunophenotypes per 5 granulocytic and 5 monocytic panels were 2.1 ± 1.2 and 2.2 ± 1.4. The rates were higher than the controls (P< 0.001, respectively). As the number of employed panels increased, the percent values of abnormal immunophenotypes increased (P=0.002). The maximum rate of abnormal immunophenotype was 89.7% in MDS patients, especially 100.0% in normal karyotype, when a combination of three panels, CD15/CD10/CD45, CD64/CD33/CD45, and either CD16/CD13/CD45 or CD16/CD11b/CD45 was used. This study demonstrates that a combination of CD15/CD10, CD64/CD33, CD16/CD13 or CD11b granulocyte panels in FCM is sensitive and specific for diagnosis of MDS.

Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria.

A multiplex real-time PCR assay and melting curve analysis for identifying 23 mycobacterial species was developed and evaluated using 77 reference strains and 369 clinical isolates. Concordant results were obtained for all 189 (100%) isolates of the Mycobacterium tuberculosis complex and 169 (93.9%) isolates of nontuberculous mycobacteria. Our results showed that this multiplex real-time PCR assay is an effective tool for the mycobacterial identification from cultures.

[Minimal residual disease detection in acute leukemia patients by flow cytometric assay of cross-lineage antigen expression].

BACKGROUND: It has been demonstrated that flow cytometric detection of minimal residual disease (MRD) has a prognostic significance in the treatment of patients with acute leukemia. We investigated the significance of flow cytometric MRD detection for the first time in Korea. METHODS: We analyzed the results of MRD detection in morphologically complete remission bone marrow aspirates from 89 patients with newly-diagnosed or relapsed acute leukemia, in which leukemic cells had cross-lineage antigen expression. Patients were grouped based on MRD frequencies: ≥ 1.0%, high MRD; <1.0%, low MRD. RESULTS: Forty-seven ALL patients consisted of 10 with high and 37 with low MRD levels. Patients with high MRD levels showed a tendency of more frequent relapse than those with low MRD levels (40.0% and 13.5%, respectively) (P=0.08). High MRD group showed a tendency of short relapse-free survival (RFS) and overall survival (OS), although the differences were not statistically significant. Forty-two AML patients consisted of 16 with high and 26 with low MRD levels. There were no correlations between the MRD levels and relapse rate, RFS or OS. AML patients with high MRD levels showed significantly higher rate of unfavorable cytogenetic risk categories and lower rate of favorable risk categories (P=0.03). CONCLUSIONS: MRD detection by flow cytometric assay of cross-lineage antigen expression would be useful in predicting treatment outcome in patients with ALL rather than AML. We expect that the establishment of the standardization of methods, time to test or antibody combination would be achieved through further trials in this country.

Evaluation of the TEST 1 erythrocyte sedimentation rate system and intra- and inter-laboratory quality control using new latex control materials.

BACKGROUND: The erythrocyte sedimentation rate (ESR) test has been considered to be a simple procedure, not requiring quality control (QC). However, QC is essential for accuracy and precision. We evaluated the TEST 1 ESR system and performed QC procedures using newly developed latex control materials in three hospitals. METHODS: Using tripotassium ethylenediaminetetraacetic acid blood samples (n=184), we compared TEST 1 ESR values with Westergren ESR data and evaluated intra-assay precision. Three levels of latex control materials were used to assess inter-assay precision. Reference range assessment was done using samples from 220 healthy individuals. Inter-laboratory QC with latex control materials in three hospitals was performed. RESULTS: Correlation between TEST 1 ESR and Westergren ESR results was good (p<0.001). Intra-assay precision [coefficients of variation (CV) 6.6%-21.7%] with patient samples and inter-assay precision (CV 0.0%-6.8%) with latex control materials were satisfactory. The reference ranges of 2-10 mm/h for males and 2-19 mm/h for females were established. Inter-laboratory QC data with latex control materials in three hospitals demonstrated good accuracy and satisfactory precision (CV 0.0%-14.4%). CONCLUSIONS: Our results demonstrate that the TEST 1 QC is reliable and the latex control materials are valuable for inter-laboratory proficiency testing.

[Detection of vancomycin-resistant enterococci using multiplex real-time PCR assay and melting curve analysis].

BACKGROUND: We developed and evaluated the utility of a multiplex real-time PCR assay that uses melting curve analysis and allows simultaneous identification of vancomycin-resistant genotypes and clinically relevant enterococci. METHODS: The specificity of the assay was tested using 4 reference strains of vancomycin-resistant enterococci (VRE) and 2 reference strains of vancomycin-susceptible enterococci. Ninety-three clinical isolates of enterococci with different glycopeptide-resistant phenotypes were genotyped and identified using a multiplex real-time PCR assay and melting curve analysis. RESULTS: Representative melting curves were obtained for Enterococcus faecium, Enterococcus faecalis, vanA-containing E. faecium, vanB-containing E. faecalis, Enterococcus gallinarum, and Enterococcus casseliflavus. Phenotypic and genotypic analysis of the isolates revealed same results for 82 enterococcal isolates, while in 4 isolates, the glycopeptide-resistant phenotypes were inconsistent with the glycopeptide-resistant genotypes and in the 4 other isolates, species could not be accurately identified. Three isolates with mixed strains, which were detected by the PCR assay, could not be correctly identified using phenotypic methods. CONCLUSIONS: VRE genotyping and identification of clinically relevant enterococci were rapidly and correctly performed using multiplex real-time PCR assay and melting curve analysis.

[Subgenotype and serotype analysis of hepatitis B virus in Korean chronic hepatitis B patients under treatment].

BACKGROUND: Hepatitis B virus (HBV) detected in Korean patients almost belongs to genotype C, which is subdivided into subgenotype C1 (or Cs) and C2 (or Ce). It was recently reported that the risk of hepatocellular carcinoma is different between subgenotype C1 and C2. Thus, we studied the distribution of subgenotypes of HBV in Korean chronic hepatitis B (CHB) patients. METHODS: Specimens of 421 patients, who were diagnosed as CHB and underwent antiviral treatment, were used. After sequence analysis for HBV S gene, subgenotype was identified through phylogenetic analysis. Utilizing the same sequence data, the distribution of serotypes was also investigated. RESULTS: Among 421 patient specimens, genotype C was found in 419 (99.5%) and genotype B in 2 (0.5%). Among the genotype C strains, 417 strains were C2 subgenotype and 2 strains were mixed subgenotypes. However, C2 was evidently found even in the mixed sequences. Serotypes of 419 HBV with genotype C were classified as follows: adr, 385 (91.9%), adw, 22 (5.3%), ayr, 2 (0.4%) and mixed serotype, 10 (2.3%). Serotype of both HBV with genotype B was adw. CONCLUSIONS: It was found that HBV detected in Korean CHB patients under treatment almost all belong to the C2 (Ce) genotype.

Erythrocyte sedimentation rate measurements by TEST 1 better reflect inflammation than do those by the Westergren method in patients with malignancy, autoimmune disease, or infection.

We compared the TEST 1 (Alifax, Padova, Italy) and Westergren methods of measuring the erythrocyte sedimentation rate (ESR) to assess inflammation. The ESR was measured by both methods in 154 blood samples from patients with malignancy (n = 69), autoimmune disease (n = 44), or infection (n = 41). Total protein, albumin, and C-reactive protein (CRP) levels were measured in each plasma sample, and albumin and alpha(1)-, alpha(2)-, beta(1)-, beta(2)-, and gamma-globulin fractions were measured by capillary electrophoresis. TEST 1 ESR values were significantly lower than the Westergren values, by 10.9 mm/h. We found that the correlations of TEST 1 ESR values with inflammatory protein levels (total protein, globulin, CRP, and alpha(1)-, alpha(2)-, beta(2)-, and gamma-globulin) were better than those obtained using the Westergren method. These findings indicate that ESR measurements by TEST 1 reflect inflammation better than do those by the Westergren method in patients with malignancy, autoimmune disease, or infection.

[Experience on identification of cross-reactive group specificity performed by anti-human globulin panel reactive antibody tests].

BACKGROUND: Panel reactive antibody (PRA) is to screen and identify HLA antibody. Majority of antibody specificities in high-PRA are directed against cross reactive group (CREG). Thus, this study was to know the advantage of identifying CREG specificity and whether antibody specificities are changed according to CREG classification. METHODS: HLA class I antibodies were identified from 159 sera from 108 patients in Asan Medical Center, who had shown more than 5% PRA by anti-human globulin (AHG)-complement-dependent cytotoxicity (CDC). Tail analysis-based computer program was developed to identify specificities, applying both Rodey (R-ABC) and Takemoto (T-ABC) classification. The results were also compared with those obtained when without CREG application (ABC). RESULTS: Among 151 cases in which HLA specificities was identified, the frequency of CREG specificity was 22.5% in R-ABC and 27.2% in T-ABC. Eleven cases showed CREG specificities only in one classification. However, the individual antigen specificities in one hand were all included in the CREG identified in the other hand. CREG specificities in samples with PRA >50% (60%) were more frequently identified than those in samples with PRA < or =50% (9%) (in R-ABC, P<0.0001). Without applying CREG to interpretation, specificity was not identified in 9 cases. CONCLUSIONS: Application of CREG enhanced the rate of antibody identification. Antibody specificities of those cases where CREG specificities were different between Rodey and Takemoto classifications were almost the same when compared at the individual antigen level. Therefore, it was thought that it makes no difference to use any one of these two classifications in interpreting PRA.

Identification of hepatitis C virus genotype 6 in Korean patients by analysis of 5' untranslated region using a matrix assisted laser desorption/ionization time of flight-based assay, restriction fragment mass polymorphism.

Previous surveys of the prevalence of hepatitis C virus (HCV) in Korea have identified types 1 and 2, but little has been said of other genotypes and viral subtypes. In this study, HCV genotypes in Korea were investigated using Restriction Fragment Mass Polymorphism (RFMP) assay, a sensitive and specific method for genotyping based on MALDI-TOF mass spectrometry. A total of 1,043 independent serum samples from HCV-infected patients were analyzed. Of interest, 15 subjects (1.4%) were determined to contain HCV genotype 6 and 46 subjects (4.4%) contained mixed genotypes with the most prevalent genotypes being HCV 1b and 2a/c (45.0% and 35.4%, respectively). The 15 subjects with HCV genotype 6 comprised eight cases of subtype 6c, including one case of mixed infection with 1b, three cases of HCV 6a, and six cases of unassigned subtypes. Sequencing corroborated the identity of genotype 6 from 13 subjects, while the line probe assay (LiPA) mis-identified them as genotype 1b. The majority (7/9) of the genotype 6 patients enrolled for interferon/ribavirin therapy, achieved a sustained virologic response. The ability of the RFMP assay to differentiate various HCV genotypes should enable better analysis of the relationship between HCV genotype and disease prognosis.

[Performance evaluation of Abbott RealTime HBV Quantification Kit for HBV viral load by real-time PCR].

BACKGROUND: Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA). METHODS: The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA). RESULTS: Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9)copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r(2)=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r(2)=0.9933). CONCLUSIONS: The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.

[Development of a system for extracting the information of candidate tumor markers reported in biomedical literatures].

BACKGROUND: Since the human genome project was completed in 2003, there have been numerous reports on cancer and related markers. This study was aimed to develop a system to extract automatically information regarding the relationship between cancer and tumor markers from biomedical literatures. METHODS: Named entities of tumor markers were recognized by both a dictionary-based method and machine learning technology of the support vector machine. Named entities of cancers were recognized by the MeSH dictionary. RESULTS: Relational and filtering keywords were selected after annotating 160 abstracts from PubMed. Relational information was extracted only when one of the relational keywords was in an appropriate position along the parse tree of a sentence with both tumor marker and disease entities. The performance of the system developed in this study was evaluated with another set of 77 abstracts. With the relational and filtering keyword used in the system, precision was 94.38% and recall was 66.14%, while without the expert knowledge precision was 49.16% and recall was 69.29%. CONCLUSIONS: We developed a system that can extract relational information between a tumor and its markers by incorporating expert knowledge into the system. The system exploiting expert knowledge would serve as a reference when developing another information extraction system in various medical fields.

Meta-analysis of the association between HLA-DRB1 allele and rheumatoid arthritis susceptibility in Asian populations.

The aims of this study were to summarize results on the association of HLA-DRB1 with rheumatoid arthritis (RA) in Asians and to determine if the shared epitope (SE) hypothesis could explain the meta-analysis results. Among the papers published between January 1987 and July 2006 on RA susceptibility in Asian-Mongoloid populations (Korean, Japanese, Chinese, and Thai), 12 were selected for the metaanalysis. Mongoloid-Asian patients with RA had significantly higher frequencies of HLA-DRB1*0101, *0401, *0410, and *1001 than controls (OR 1.5-2.1, p<0.05 for association). When analyses were restricted to more ethnically homogeneous populations, HLA-DRB1*0405 showed a significant susceptibility to RA in Koreans (OR 5.65, 95% CI 4.32-7.39), whereas the HLA-DRB1*0301, *0403, *0406, *0701, *1301, and *1405 alleles showed protective association with RA (OR 0.32-0.70, p<0.05 for association). In conclusion, it was found that HLA-DRB1 *0101, *0401, *0405, *0410, and *1001 are susceptible, while HLA-DRB1* 0301, *0403, *0406, *0701, *1301, and *1405 are protective in Asian-Mongoloids. All the RA-associated alleles except DRB1*0301 could be explained by the structural model supporting the SE hypothesis that RA susceptibility is determined by the combination of amino acid residues at HLA-DR beta71 and beta74, not by beta71 alone.