Increased rate of CD4+ T-cell decline and faster time to antiretroviral therapy in HIV-1 subtype CRF01_AE infected seroconverters in Singapore.

BACKGROUND: It remains controversial as to whether HIV-1 subtypes influence disease progression. Singapore offers a unique opportunity to address this issue due to the presence of co-circulating subtypes. We compared subtype CRF01_AE and non-CRF01_AE infected patients, with regards to estimated annual rate of CD4+ T-cell loss and time from estimated data of seroconversion (EDS) to antiretroviral therapy (ART). METHODS: We recruited ART-naive patients with known dates of seroconversion between October 2002 and December 2007 at the Singapore Communicable Disease Centre, the national reference treatment centre. Multilevel mixed-effects models were used to analyse the rate of CD4+ T-cell decline. Time from EDS to ART was analyzed with the Kaplan-Meier survival method and compared with Cox proportional hazards models. RESULTS: 54 patients with previously assigned HIV-1 subtypes (24 CRF01_AE, 17 B, 8 B', 1 CRF33_01B, 3 CRF34_01B and 1 G) were observed for 89 patient-years. Subtype CRF01_AE and non-CRF01_AE infected patients did not differ in age, gender, risk factor, rate of symptomatic seroconversion, baseline CD4+ T-cell count, log(10) viral load or haemoglobin concentration. The estimated annual rate of CD4+ T-cell loss was 58 cells/mm(3)/year (95% CI: 7 to 109; P = 0.027) greater in subtype CRF01_AE infected patients compared to non-CRF01_AE patients, after adjusting for age, baseline CD4+ T-cell count and baseline log(10) viral load. The median time from EDS to ART was 1.8 years faster comparing CRF01_AE to non-CRF01_AE infected patient with a 2.5 times (95% CI: 1.2-5.0; P = 0.013) higher hazard for ART initiation, after controlling for age, baseline CD4+ T-cell count and baseline log(10) viral load. CONCLUSIONS: Infecting subtype significantly impacted the rate of CD4+ T-cell loss and time to treatment in this cohort. Studies to understand the biological basis for this difference could further our understanding of HIV pathogenesis.

Contribution of dfrA and inhA mutations to the detection of isoniazid-resistant Mycobacterium tuberculosis isolates.

Screening of 127 isoniazid (INH)-resistant Mycobacterium tuberculosis isolates from Singapore for mutations within the dfrA and inhA genes revealed mutations in 0 and 5 (3.9%) isolates respectively, implying that mutations in dfrA do not contribute to the detection of INH-resistant M. tuberculosis and that mutations within inhA are rare. Thirty-seven (29%) of the 127 isolates had no mutations in any of the genes implicated in INH resistance (katG, kasA, and ndh; inhA and ahpC promoters), suggesting that there are new INH targets yet to be discovered.

IL-1beta, IL-6, and RANTES as biomarkers of Chikungunya severity.

BACKGROUND: Little is known about the immunopathogenesis of Chikungunya virus. Circulating levels of immune mediators and growth factors were analyzed from patients infected during the first Singaporean Chikungunya fever outbreak in early 2008 to establish biomarkers associated with infection and/or disease severity. METHODS AND FINDINGS: Adult patients with laboratory-confirmed Chikungunya fever infection, who were referred to the Communicable Disease Centre/Tan Tock Seng Hospital during the period from January to February 2008, were included in this retrospective study. Plasma fractions were analyzed using a multiplex-microbead immunoassay. Among the patients, the most common clinical features were fever (100%), arthralgia (90%), rash (50%) and conjunctivitis (40%). Profiles of 30 cytokines, chemokines, and growth factors were able to discriminate the clinical forms of Chikungunya from healthy controls, with patients classified as non-severe and severe disease. Levels of 8 plasma cytokines and 4 growth factors were significantly elevated. Statistical analysis showed that an increase in IL-1beta, IL-6 and a decrease in RANTES were associated with disease severity. CONCLUSIONS: This is the first comprehensive report on the production of cytokines, chemokines, and growth factors during acute Chikungunya virus infection. Using these biomarkers, we were able to distinguish between mild disease and more severe forms of Chikungunya fever, thus enabling the identification of patients with poor prognosis and monitoring of the disease.

A comparative study of polymerase chain reaction detection of clonal T-cell receptor gamma chain gene rearrangements using polyacrylamide gel electrophoresis versus fluorescence capillary electrophoresis.

INTRODUCTION: Polymerase chain reaction (PCR)-based molecular techniques are useful adjunctive tools in the diagnosis of cutaneous T-cell lymphomas (CTCL). This study compares the sensitivity of PCR analysis of the T-cell receptor-gamma (TCR-gamma) gene rearrangements using conventional polyacrylamide gel electrophoresis (PCR-PAGE) and fluorescent capillary electrophoresis (PCR-FCE). MATERIALS AND METHODS: A total of 22 paraffin blocks were analysed using PCR-PAGE and PCR-FCE. There were 17 cases of mycosis fungoides (MF), 4 cases of non-MF CTCL and 1 case of lymphoblastic leukaemia. RESULTS: Complete agreement was obtained between PCR-PAGE and PCR-FCE in 19 of the 22 cases, giving a concordance rate of 86.4%. PCR-FCE had a higher sensitivity of 77.3%, compared to 63.6% for PCR-PAGE, allowing the detection of 3 additional cases of clonal T-cell rearrangements, which had equivocal or polyclonal bands on PAGE. Two of these 3 cases were in erythrodermic MF patients. PCR-FCE also allowed the detection of matching clones in serial specimens taken from different sites and at different time intervals in patients with MF. However, matching clones from different specimens can be achieved qualitatively in PCR-PAGE by running and comparing these on the same polyacrylamide gel block. CONCLUSIONS: Both PCR-PAGE and PCR-FCE are useful in detecting T-cell clones in CTCL, with both methods being comparable in sensitivity and showing a high concordance rate of 86.4%. PCR-FCE has the added advantage of exhibiting semiquantitative properties, which may be important in early or erythrodermic MF cases, but the requirement for sophisticated and costly machinery limits its availability to high-capacity laboratories. The well-established PCR-PAGE method is a suitable alternative in routine clinical applications.

T-cell receptor-gamma gene analysis in evolving to advancing cutaneous T-cell lymphoma.

The diagnosis of cutaneous T-cell lymphoma is often a challenge for the dermatopathologist. Early stages can mimic inflammatory dermatoses. Our aim was to explore the applicability of a standard T-cell receptor-gamma polymerase chain reaction in various subtypes of cutaneous T-cell lymphomas. Ninety-six biopsy specimens from 38 patients were selected. These included 72 specimens of mycosis fungoides, 12 specimens of non-mycosis fungoides T-cell lymphomas, and 12 specimens in which histology was non-specific or equivocal in patients who were later diagnosed to have lymphoma. T-cell clones were detected in 53 of 72 specimens of mycosis fungoides and eight of 12 specimens of non-mycosis fungoides lymphomas. Of the 72 specimens of mycosis fungoides, T-cell clones were detected in eight of 10 specimens of mycosis fungoides-associated follicular mucinosis and pigmented purpura-like mycosis fungoides. Four specimens from the 12 prediagnostic for cutaneous T-cell lymphomas showed presence of T-cell clones, identical to subsequent clones detected when lymphoma was fully established. In specimens where histology is not diagnostic and T-cell receptor-gamma gene analysis is positive, patients should be followed up closely. T-cell receptor-gamma gene analysis is a useful adjunct to histological diagnosis of early stage and variant types of mycosis fungoides.

Tuberculosis associated with Mycobacterium tuberculosis Beijing and non-Beijing genotypes: a clinical and immunological comparison.

BACKGROUND: The Mycobacterium tuberculosis Beijing genotype is biologically different from other genotypes. We aimed to clinically and immunologically compare human tuberculosis caused by Beijing and non-Beijing strains. METHODS: Pulmonary tuberculosis patients were prospectively enrolled and grouped by their M. tuberculosis genotypes. The clinical features, plasma cytokine levels, and cytokine gene expression levels in peripheral blood mononuclear cells (PBMC) were compared between the patients in Beijing and non-Beijing groups. RESULTS: Patients in the Beijing group were characterized by significantly lower frequency of fever (odds ratio, 0.12, p = 0.008) and pulmonary cavitation (odds ratio, 0.2, p = 0.049). Night sweats were also significantly less frequent by univariate analysis, and the duration of cough prior to diagnosis was longer in Beijing compared to non-Beijing groups (medians, 60 versus 30 days, p = 0.048). The plasma and gene expression levels of interferon (IFN) gamma and interleukin (IL)-18 were similar in the two groups. However, patients in the non-Beijing group had significantly increased IL-4 gene expression (p = 0.018) and lower IFN-gamma : IL-4 cDNA copy number ratios (p = 0.01). CONCLUSION: Patients with tuberculosis caused by Beijing strains appear to be less symptomatic than those who have disease caused by other strains. Th1 immune responses are similar in patients infected with Beijing and non-Beijing strains, but non-Beijing strains activate more Th2 immune responses compared with Beijing strains, as evidenced by increased IL-4 expression.

Mimotopes for lupus-derived anti-DNA and nucleosome-specific autoantibodies selected from random peptide phage display libraries: facts and follies.

Autoantibodies against chromatin are the most characteristic serological feature in SLE patients. Anti-dsDNA and nucleosome-specific antibodies are associated with glomerulonephritis, the most serious manifestation of SLE. Identification of peptides mimicking conformational epitopes (so-called mimotopes) on the nucleosome recognized by these antibodies is of considerable interest. Using an approach similar to that used previously to characterize mimotopes for anti-DNA autoantibodies, we have selected and identified a mimotope for a nucleosome-specific autoantibody (#32) by screening a random peptide phage display library. However, the reactivity of monoclonal antibody (mAb) #32 with the selected mimotope (MIMO#0) in ELISA was dependent on the blocking reagents used. Using nonfat dry milk (5%), mAb #32 clearly bound to MIMO#0, but using fetal bovine calf serum (FCS) (5%), there was no binding. Furthermore, again dependent on the blocking reagent used in ELISA, the selected mimotope MIMO#0 was not only recognized by the selecting antibody mAb #32, but also by a large number of other monoclonal anti-DNA, anti-histone and nucleosome-specific autoantibodies (NSA). We could demonstrate that the selected mimotope was able to bind directly to nucleosomal material (DNA/histone complexes) and labeled DNA. This finding was extended to other previously identified mimotopes for anti-DNA autoantibodies. We conclude that nucleosomal material (DNA/histone complexes), derived from reagents used during the mimotope selection procedure, resulted in the selection of DNA-binding peptides from the phage display library, rather than mimotopes. In addition, we could demonstrate that blocking reagents greatly influence the reactivity of anti-DNA, anti-histone and nucleosome-specific autoantibodies in ELISA. Development of blocking reagents devoid of nucleosomal material (DNA/histone complexes) is urgently needed for assay systems in which anti-nuclear autoantibodies are tested.

Characterization of ancestral Mycobacterium tuberculosis by multiple genetic markers and proposal of genotyping strategy.

Sixty-eight ancestral Mycobacterium tuberculosis isolates were previously identified by using the tuberculosis-specific deletion 1 (TbD1) PCR and mycobacterial interspersed-repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing (Y. J. Sun, R. Bellamy, A. S. G. Lee, S. T. Ng, S. Ravindran, S.-Y. Wong, C. Locht, P. Supply, and N. I. Paton, J. Clin. Microbiol. 42:1986-1993, 2004). These TbD1(+) ancestral isolates were further characterized and typed in this study by IS6110 restriction fragment length polymorphism (RFLP) typing, VNTR typing using exact tandem repeats (VNTR-ETR), and spoligotyping of the direct-repeat region. To our knowledge, this is the first characterization of this genogroup by multiple genetic markers based on a fairly large sample size. In this genogroup, all spoligotypes were characterized by the absence of spacers 29 to 32 and 34. In addition, VNTR-ETR typing could add further resolution to the clustered isolates identified by MIRU-VNTR, and the combination of MIRU-VNTR and VNTR-ETR, called MIRU-ETR, showed the highest discriminatory power for these strains compared to IS6110 RFLP typing and spoligotyping alone. However, MIRU-ETR appeared to still cluster some probably epidemiologically unrelated strains, as judged by IS6110 RFLP divergence. Therefore, a typing strategy based on stepwise combination of MIRU-ETR and IS6110 RFLP is proposed to achieve maximal discrimination for unrelated TbD1(+) strains. This typing strategy may be useful in areas where TbD1(+) ancestral strains are prevalent.

Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore.

Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.

Detection of herpes simplex virus genomic DNA in various subsets of Erythema multiforme by polymerase chain reaction.

BACKGROUND: The wide variation in the detection of herpes simplex virus (HSV) DNA (36-75%) by polymerase chain reaction (PCR) in erythema multiforme (EM) may be partly attributed to differences in case selection in terms of subsets of EM studied. OBJECTIVE: To determine the frequencies of detection of HSV DNA in specific subsets of EM. METHODS: Nested PCR was used to detect HSV DNA in skin biopsies with histologically proven EM. RESULTS: PCR was performed on skin biopsies from 63 patients with EM. HSV DNA was detected in 3/11 (27.2%) of single-episode HSV-associated EM (HAEM), 6/10 (60%) of recurrent HAEM, 1/4 (25%) of single-episode idiopathic EM and 6/12 (50%) of recurrent idiopathic EM. HSV DNA was not detected in atypical EM (0/11), suspected drug-induced EM (0/9) or Stevens-Johnson syndrome (0/6). CONCLUSION: The overall PCR positive rates of HAEM (42.9%) and idiopathic EM (43.8%) were comparable suggesting that idiopathic EM is likely to be related to a subclinical HSV infection.