Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting

INTRODUCTION:

Nontuberculous mycobacteria (NTM) species, as human pathogens, are increasing in the world, as is the difficulty of accurately identifying them. Differential diagnosis, especially between the M. tuberculosis complex and NTM species, and the characterization of NTM species is important. This study aimed to evaluate the performance of a molecular system based on multiplex real-time PCR with high-resolution melting (HRM) for the identification and differentiation of NTM species of clinical importance of an endemic area for tuberculosis in northeastern Brazil.

METHODS:

The technical protocol of the molecular system was based on multiplex real-time PCR-HRM, and evaluated the sensitivity and specificity of the detection of NTM species in mycobacterial clinical isolates from the studied region. The gold standard method was specific gene sequencing.

RESULTS:

The sensitivity and specificity of multiplex real-time PCR-HRM modified for differentiation between NTM and M. tuberculosis were 90% and 100%, respectively. The PCR-HRM sensitivities for the characterization of NTM species (M. kansasii, M. abscesses, M. avium, and M. fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively.

CONCLUSIONS

The multiplex real-time PCR-HRM modified assay has the potential to rapidly and efficiently identify nontuberculous mycobacteria of clinical importance, which is crucial for immediate implementation of the appropriate therapy and thus avoiding complications and sequelae in patients.

Discovery of a novel Mycobacterium asiaticum PRA-hsp65 pattern

Twenty-one pulmonary sputum samples from nine Brazilian patients were analyzed by the PRA-hsp65 method for identification of Mycobacterium species and the results were compared by sequencing. We reported a mutation at the position 381, that generates a suppression cutting site in the BstEII enzyme, thus leading to a new PRA-hsp65 pattern for M. asiaticum identification.

Drug susceptibility profile of Mycobacterium kansasii clinical isolates from Brazil

OBJECTIVES

Mycobacterium kansasii (M. kansasii) pulmonary infection can cause disease with clinical and radiological features similar to tuberculosis. Failure to treat M. kansasii infection is usually associated with resistance; to increase the chance of successful treatment it is important to identify the species and know the susceptibility profile. This study aimed to evaluate the antimycobacterial susceptibility profiles of M. kansasii isolates from Brazil.

METHODS

Sixty-nine M. kansasii isolates from 69 patients were identified by partial sequencing of the hsp65 gene, and their susceptibility profiles were analysed by minimal inhibitory concentration (MIC) assays.

RESULTS

From 69 isolates, 68 showed susceptibility to clarithromycin, amikacin, and moxifloxacin. Most strains showed high rates of resistance to trimethoprim-sulfamethoxazole and ciprofloxacin. Resistance to rifampicin and ethambutol was found in 12% and 25% of isolates, respectively.

CONCLUSIONS

Worrying results were found regarding susceptibility to some drugs used as first-line agents in the treatment of diseases caused by M. kansasii.

Effects of cytochalasin E on Paracoccidioides brasiliensis

AIMS

To determine the effects of cytochalasin E, isolated from the extremophile fungus Aspergillus felis, on the cells of Paracoccidioides brasiliensis Pb18.

METHODS AND RESULTS

Cytochalasin E showed a minimal inhibitory concentration of 3·6 μmol l^-1 and minimum fungicidal concentration of 7·2 μmol l^-1 on P. brasiliensis by in vitro microdilution and IC₅₀ >964·0 μmol l^-1 on murine macrophages. Its selectivity index (>263) indicated that this compound has selectivity for fungal cells. Morphological alterations were determined by optical and fluorescence microscopy, as well as scanning and transmission electron microscopy. Cytochalasin E affected P. brasiliensis bud-forming pseudohyphae, cell morphology, cell walls and cell membranes; caused the release of cellular material; and resulted in the production of reactive oxygen species. In murine macrophages, it affected cytoskeletal actin and inhibited phagocytosis.

CONCLUSION

Cytochalasin E may be useful as an antifungal prototype against P. brasiliensis and in studies on phagocytosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

Paracoccidioides spp. are the etiological agents of paracoccidioidomycosis (PCM). Treatment is prolonged to control the clinical manifestations and prevent relapse. The study on the effects of cytochalasin E in P. brasiliensis is important because it can be used as a prototype for new antifungal drugs and consequently, broadens the treatment options for PCM.

Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity

Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil.

Factors associated with loss to follow-up and death in cases of drug-resistant tuberculosis (DR-TB) treated at a reference center in Rio de Janeiro, Brazil

Drug-resistant tuberculosis (DR-TB) poses a serious threat to tuberculosis (TB) control in Brazil and worldwide. The current study investigated factors associated with loss to follow-up and death in the course of treatment for DR-TB in a tertiary reference center in the city of Rio de Janeiro, Brazil. This was a retrospective cohort study of cases reported to the Information System on Special Treatments for Tuberculosis (SITETB) from January 1, 2012, to December 31, 2013. A total of 257 patients were reported to the SITETB and initiated treatment for DR-TB. Of this total, 139 (54.1%) achieved treatment success as the outcome, 54 (21%) were lost to follow-up, and 21 (8.2%) died. Following a multiple multinomial logistic regression analysis, the age bracket older than 50 years was the only protective factor against loss to follow-up, whereas less than eight years of schooling and reentry after loss to follow-up were considered risk factors. Reentry after loss to follow-up, relapse, and treatment failure appeared as risk factors. Our data reinforce the concept that loss to follow-up in drug-resistant tuberculosis is a serious public health problem, and that adequate follow-up of treatment is necessary in patients with this history and low schooling. A social support network for patients is also indispensable for avoiding unfavorable outcomes.

Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil

An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical distribution across Brazil is due to spread from a single point source or is the result of human-mediated transmission. 188 isolates, collected from nine Brazilian states, were whole genome sequenced and analysed using phylogenetic and comparative genomic approaches. The isolates from Brazil formed a single clade, which was estimated to have emerged in 2003. We observed temporal and geographic structure within the lineage that enabled us to infer the movement of sub-lineages across Brazil. The genome size of the Brazilian lineage was reduced relative to most strains in the three subspecies of Mycobacterium abscessus and contained a novel plasmid, pMAB02, in addition to the previously described pMAB01 plasmid. One lineage, which emerged just prior to the initial outbreak, is responsible for the epidemic of post-surgical wound infections in Brazil. Phylogenetic analysis indicates that multiple transmission events led to its spread. The presence of a novel plasmid and the reduced genome size suggest that the lineage has undergone adaptation to the surgical niche.

Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov., two tremellaceous yeast species from Brazil

Two yeast species, Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov., in the family Rhynchogastremataceae of the Tremellales are proposed. The two species are related to six species of the genus Papiliotrema: Papiliotrema aureus, P. flavescens, P. terrestris, P. baii, P. ruineniae and P. wisconsinensis. The novel species are proposed on the basis of the sequence-based phylogenetic species concept with analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. A total of 16 strains of Papiliotrema leoncinii sp. nov. were obtained from freshwater and bromeliad leaves collected in Brazil. Papiliotrema leoncinii sp. nov. differs by 11, 12, 16, 14, 11 and 13 substitutions in the D1/D2 domain from the related species P. aureus, P. flavescens, P. terrestris, P. baii, P. ruineniae and P. wisconsinensis, respectively. Differences of 11 substitutions and 21 or more substitutions in ITS regions were found when the sequences of Papiliotrema leoncinii sp. nov. were compared with P. wisconsinensis and its closest relatives. The type strain of Papiliotrema leoncinii sp. nov. is UFMG-CM-Y374T (=CBS 13918T). Papiliotrema miconiae sp. nov. is represented by two strains isolated from a flower of Miconia sp. and a water sample in Brazil. Papiliotrema miconiae sp. nov. differs from the related species P. aureus and P. ruineniae by eight substitutions, from P. flavescens and P. terrestris by 11 substitutions, from P. baii by 10 substitutions and from P. wisconsinensis by 6 substitutions in the D1/D2 domain, and by 7 substitutions from P. wisconsinensis and more than 19 substitutions in the ITS region from its closest relatives. The type strain of Papiliotrema miconiae sp. nov. is CBS 8358T (ML 3666T=DBVPG-4492T). The MycoBank numbers for Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov. are MB 813594 and MB 814882, respectively.

Nontuberculous mycobacteria in respiratory samples from patients with pulmonary tuberculosis in the state of Rondônia, Brazil

The main cause of pulmonary tuberculosis (TB) is infection with Mycobacterium tuberculosis (MTB). We aimed to evaluate the contribution of nontuberculous mycobacteria (NTM) to pulmonary disease in patients from the state of Rondônia using respiratory samples and epidemiological data from TB cases. Mycobacterium isolates were identified using a combination of conventional tests, polymerase chain reaction-based restriction enzyme analysis of hsp65 gene and hsp65 gene sequencing. Among the 1,812 cases suspected of having pulmonary TB, 444 yielded bacterial cultures, including 369 cases positive for MTB and 75 cases positive for NTM. Within the latter group, 14 species were identified as Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium intracellulare, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium asiaticum, Mycobacterium tusciae, Mycobacterium porcinum, Mycobacterium novocastrense, Mycobacterium simiae, Mycobacterium szulgai, Mycobacterium phlei and Mycobacterium holsaticum and 13 isolates could not be identified at the species level. The majority of NTM cases were observed in Porto Velho and the relative frequency of NTM compared with MTB was highest in Ji-Paraná. In approximately half of the TB subjects with NTM, a second sample containing NTM was obtained, confirming this as the disease-causing agent. The most frequently observed NTM species were M. abscessus and M. avium and because the former species is resistant to many antibiotics and displays unsatisfactory cure rates, the implementation of rapid identification of mycobacterium species is of considerable importance.

Rapid tests for the detection of the Mycobacterium abscessus subsp. bolletii strain responsible for an epidemic of surgical-site infections in Brazil

A single strain of Mycobacterium abscessus subsp. bolletii, characterised by a particular rpoB sequevar and two highly related pulsed field gel electrophoresis patterns has been responsible for a nationwide outbreak of surgical infections in Brazil since 2004. In this study, we developed molecular tests based on polymerase chain reaction restriction-enzyme analysis (PRA) and sequencing for the rapid identification of this strain. Sequences of 15 DNA regions conserved in mycobacteria were retrieved from GenBank or sequenced and analysed in silico. Single nucleotide polymorphisms specific to the epidemic strain and located in enzyme recognition sites were detected in rpoB, the 3' region of the 16S rDNA and gyrB. The three tests that were developed, i.e., PRA-rpoB, PRA-16S and gyrB sequence analysis, showed 100%, 100% and 92.31% sensitivity and 93.06%, 90.28% and 100% specificity, respectively, for the discrimination of the surgical strain from other M. abscessus subsp. bolletii isolates, including 116 isolates from 95 patients, one environmental isolate and two type strains. The results of the three tests were stable, as shown by results obtained for different isolates from the same patient. In conclusion, due to the clinical and epidemiological importance of this strain, these tests could be implemented in reference laboratories for the rapid preliminary diagnosis and epidemiological surveillance of this epidemic strain.

Nontuberculous mycobacteria in respiratory samples from patients with pulmonary tuberculosis in the state of Rondônia, Brazil

The main cause of pulmonary tuberculosis (TB) is infection with Mycobacterium tuberculosis (MTB). We aimed to evaluate the contribution of nontuberculous mycobacteria (NTM) to pulmonary disease in patients from the state of Rondônia using respiratory samples and epidemiological data from TB cases. Mycobacterium isolates were identified using a combination of conventional tests, polymerase chain reaction-based restriction enzyme analysis of hsp65 gene and hsp65 gene sequencing. Among the 1,812 cases suspected of having pulmonary TB, 444 yielded bacterial cultures, including 369 cases positive for MTB and 75 cases positive for NTM. Within the latter group, 14 species were identified as Mycobacterium abscessus, Mycobacterium avium, Mycobacterium fortuitum, Mycobacterium intracellulare, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium asiaticum, Mycobacterium tusciae, Mycobacterium porcinum, Mycobacterium novocastrense, Mycobacterium simiae, Mycobacterium szulgai, Mycobacterium phlei and Mycobacterium holsaticum and 13 isolates could not be identified at the species level. The majority of NTM cases were observed in Porto Velho and the relative frequency of NTM compared with MTB was highest in Ji-Paraná. In approximately half of the TB subjects with NTM, a second sample containing NTM was obtained, confirming this as the disease-causing agent. The most frequently observed NTM species were M. abscessus and M. avium and because the former species is resistant to many antibiotics and displays unsatisfactory cure rates, the implementation of rapid identification of mycobacterium species is of considerable importance.

Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens

Three isolates of a slow-growing, non-chromogenic mycobacterium were grown from three sputum samples of a patient from the north-eastern Ceará state in Brazil. Identification at species level could not be obtained with PCR restriction analysis of the hsp65 gene. In order to characterize the isolates we carried out phenotypic and genotypic tests. We sequenced the nearly complete 16S rRNA gene and obtained partial sequences of the hsp65 (encoding the hypervariable region of the 65 kDa heat-shock protein) and rpoB (encoding the beta-subunit of RNA polymerase) genes. The three isolates turned out to be identical and most closely related to the species Mycobacterium celatum and Mycobacterium kyorinense. The results, however, showed significant differences between these species and the isolates studied, which led us to consider them members of a novel species for which we propose the name Mycobacterium fragae. The type strain is HF8705(T) ( = Fiocruz-INCQS/CMRVS P4051(T) = DSM 45731(T)).

Modulation filtering for noise detection in heart sound signals

Cardiac auscultation has proven to be an excellent diagnostic tool. Heart sound processing algorithms are not completely robust in the presence of noise, requiring clean segments of heart sounds to extract reliable diagnostic features. This paper presents a new approach to detect transient noises mixed with heart sound. The algorithm explores a single channel source separation algorithm and evaluates the non-stationary separated signals. It has the potential to be applied in real-time. Using a database of heart sounds acquired in real-life scenario, the method showed a sensitivity and a specificity of 93.6% and 92.3%, respectively.

Heteroduplex mobility assay of the D1/D2 region of the 26S rDNA for differentiation of Saccharomyces species

AIMS

We present the HMA method for Saccharomyces differentiation using the PCR amplified D1/D2 26S rDNA.

METHODS AND RESULTS

This methodology is based on heteroduplex formation when two different DNAs are hybridized. We tested 11 type cultures of Saccharomyces, 27 different cultures of S. cerevisiae and four other ascomycetic genera.

CONCLUSION

The method was capable of differentiating Saccharomyces species and was mainly very efficient for S. cerevisiae identification. HMA can probably be applied in other genera, where identification is sometimes difficult only by conventional traits, which are based on physiology and morphology.

SIGNIFICANCE AND IMPACT OF THE STUDY

HMA provides a rapid and relatively simple molecular tool, contributing for yeast taxonomy.

Microemulsion cyclosporin formulation, in contrast to the old formulation, widens the T lymphocyte subsets differences between stable and acute rejection of kidney transplants

BACKGROUND

The new cyclosporin (CsA) formulation, Neoral, has different pharmacokinetics compared with Sandimmune (SIM). Larger area under the curve (AUC) values with equivalent trough blood values are reached when Neoral is administered at equivalent doses to SIM. Previously, we showed a great diagnostic reliability when using cytofluorometric analysis from fine-needle aspiration biopsy (FNAB) samples. We investigated possible changes brought about by Neoral on lymphocyte subsets and the repercussions on the activation score cut-off for acute rejection, defined under SIM treatment.

METHODS

Of 63 patients that received SIM, 40 remained rejection-free and 23 suffered one episode of rejection. Of 52 patients that received Neoral, 38 remained rejection-free. Peripheral blood lymphocytes (PBL) and lymphocytes from FNAB taken on days 7 and 14 post-transplantation and on the first day of acute rejection were analysed by flow cytometry.

RESULTS

Trough blood CsA levels were not different between SIM and Neoral treatments. Among rejection-free patients, a significant down-regulation of CD3DR and of CD8DR expression on both graft-infiltrating lymphocytes (GIL) and PBL, and significant up-regulation of naïve T cells on GIL were observed with Neoral. These changes were followed by a significant down-regulation of the activation score with Neoral. Conversely, within the acute rejection group, the activation score was significantly higher with Neoral than with SIM. The activation score performed equally well in Neoral transplants compared with what we had reported with SIM.

CONCLUSIONS

Our study indicates that Neoral elicits stronger immunosuppressive effects in stable patients, which eventually should translate into better clinical efficiency. However, when acute rejection supervenes, the treatment breakthrough seems stronger with Neoral. Cytofluorometric studies from FNAB samples showed that diagnostic reliability was maintained at a high level under Neoral therapy.

Sequencing as a tool in yeast molecular taxonomy

The literature on sequencing as a tool for yeast molecular taxonomy is reviewed. Ribosomal DNA has been preferred for sequencing over other molecules such as mitochondrial DNA, and a large database is now available. rDNA consists of regions that evolve at different rates, allowing comparison of different levels of relationship among yeasts. Sequences of the 18S rDNA and the 25S rDNA have been largely used for yeast systematics and phylogeny, but the search for regions with increased resolving power has led to the study of the spacer regions of the rDNA. Few studies are concerned with signature sequences.

T lymphocyte subsets and cytokine production by graft-infiltrating cells in FSGS recurrence post-transplantation

BACKGROUND

Focal segmental glomerulosclerosis (FSGS) aetiology remains undefined although a derangement of lymphocytes and monocytes macrophages, at least, has been strongly suspected. We report the graft-infiltrating phenotypes and their cytokine production in a case of FSGS recurrence post-transplantation.

METHODS

The kidney transplant recipient suffered immediate FSGS recurrence. Aspiration biopsies were done at the first and second week post-surgery and were analysed by flow cytometry. The cytokine analysis was done on aspiration sample culture supernatants and serum by enzyme-linked immunosorbent assay.

RESULTS

High expression of CD3CD69, CD3CD71 and CD4CD29 was found on infiltrating lymphocytes. Biopsy cultures pointed to a Th0/Th1 pattern of cytokine production as well as significant synthesis of transforming growth factor-beta1. Interestingly, monocyte chemokines were absent.

CONCLUSION

We report evidence of intragraft lymphocyte activation in the early days of FSGS recurrence. Aspiration biopsy cultures showed failure of cyclosporin A to inhibit interleukin-2 (IL-2) production by infiltrating lymphocytes. If our findings are confirmed in similar patients, a trial with anti-IL-2-receptor antibody could be warranted.

Analysis of fine-needle aspiration biopsies by flow cytometry in kidney transplant patients

BACKGROUND

Peripheral blood lymphocyte (PBL) analysis by flow cytometry has been inconsistently reported as an adjunctive method for diagnosing acute kidney transplant rejection. However, there is good evidence that lymphocytes infiltrating renal grafts differ from those found at the peripheral level. We hypothesized that the study of aspiration biopsy samples in conjunction with PBL by flow cytometry would enable us to diagnose acute rejection crisis reliably.

METHODS

Lymphocytes from PBL and aspiration biopsies of kidney transplant patients were analyzed. Fifty-one stable patients, rejection-free for the first 6 months, were studied on day 7 and day 30 after transplantation and were compared with 32 patients with 40 acute rejection episodes.

RESULTS

Significant differences were observed for several lymphocyte subpopulations on aspiration biopsy samples comparing stable patients with rejection patients. In contrast, PBL analysis was not helpful in differentiating the two groups of patients. By combining the expression of several activation markers inside the graft with CD3DR and CD3CD25 aspiration biopsy to peripheral blood ratios, we obtained very good values for sensitivity and specificity-83.9% and 90.5%, respectively. The positive predictive value for rejection among dysfunctional grafts reached 85.8%.

CONCLUSIONS

Flow cytometry study of aspiration biopsy samples of kidney transplant patients is a reliable and powerful method to diagnose acute rejection episodes, although it is needed to consider several lymphocyte phenotypes; cytofluorometric analysis of PBL is important because it provides graft-infiltrating cell to peripheral blood lymphocyte ratios. This safe and rapid test may significantly improve the management of kidney transplant patients.

[Rate of protein catabolism as an indicator of protein ingestion in uremic patients on hemodialysis]

Protein catabolic rate (PCR) has been proposed as a indirect index of dietary protein intake, but its sensitivity has been discussed. In a group of 140 chronic uremic patients undergoing maintenance hemodialysis, we evaluated the nutritional status (body mas index: BMI, triceps skinfold thickness: TST, arm muscle circumference: AMC, serum total proteins, albumin and lymphocytes) and its relation with dietary survey and PCR levels. PCR was correlated positively with Kt/V (p: 0.0001, r: 0.45) and with seric albumin (p: 0.01, r: 0.22), whereas dietary protein intake by dietary survey (g/Prot/Kg/day) was correlated strongly with anthropometric measurements like BMI, AMC (p: 0.0001) and less with Kt/V (p: 0.01), but not with serum albumin. PCR was correlated with dietary survey results: g Prot/Kg/day (p: 0.04, r: 0.18) and Kcal/Kg/day (p: 0.03, r:0.2). The results suggest that nutritional parameters with slow evolution as anthropometric measurements could be related with usual dietary intake (dietary survey), whereas serum albumin (that vary early with recent changes of dietary intake) could be related better with a biochemical index like PCR, in these way both determinations are complementary.

Cutaneous T-cell recruitment in toxic epidermal necrolysis. Further evidence of CD8+ lymphocyte involvement

BACKGROUND

Toxic epidermal necrolysis (TEN) is a life-threatening disease with severe mucocutaneous shedding. Although it is widely accepted that immune mechanisms are at play, the pathophysiology of TEN is still unknown. We studied the blister fluid inflammatory cells in three drug-related cases to further define the suspected T-cell involvement in TEN.

OBSERVATIONS

A peripheral blood lymphopenia, especially of CD4+ T lymphocytes, was associated with a high lymphocytic cellularity of the blister fluid. In two cases, immunophenotyping of blister fluid lymphocytes showed a predominance of the CD8 phenotype. Furthermore, using two-color flow cytometry in one patient, we could show the predominance of CD8+ CD29+ lymphocytes and CD45RA- negative cells.

CONCLUSIONS

Our findings point to a cutaneous recruitment of antigen-primed and cytotoxic T cells in TEN, further supporting the involvement of CD8+ lymphocytes in TEN pathogenesis and its immune mediation.