Cutaneous non-tuberculous Mycobacterial infections: a clinical and histopathological study of 17 cases from Lebanon.

BACKGROUND: Only a few studies characterized cutaneous non-tuberculous Mycobacterium (NTM) infections in this region of the world. Objective The aim of this study was to describe the epidemiological, clinical and histological findings of cutaneous NTM infections in Lebanon. PATIENTS/METHODS: Retrospective study of 17 patients (19 histological specimens) diagnosed with cutaneous NTM infections and confirmed by culture-based partial sequencing of the 16S rRNA gene at the American University of Beirut Medical Center between 2005 and 2008. RESULTS: Of 17 cases, 14 were caused by Mycobacterium marinum. All patients were immunocompetent except for one. Clinically, the most common presentation was multiple sporotrichoid lesions over an extremity (8/17). Many patients had peculiar presentations including bruise-like patches, herpetiform lesions, annular ulcerated plaques, symmetrical nodules over the buttocks and locally disseminated lesions with surrounding pale halo. Almost all patients cleared their infection on either minocycline or clarithromycin monotherapies. Histologically, a dermal small vessel proliferation with mixed inflammation (granulation tissue-like changes) was identified in 58% of specimens. The most common type of granulomatous inflammation was the suppurative (47%) followed by the tuberculoid (30%), sarcoidal (11%), and palisading (5%) types. Lichenoid granulomatous dermatitis was noted in 42% of cases. Special staining highlighted mycobacteria in only two specimens. CONCLUSIONS: The incidence of cutaneous NTM infections is high in our area. Many patients had peculiar clinical presentations. Our study is the second to report the common presence of granulation tissue-like changes as a good histological indicator of cutaneous NTM infections. Minocycline and clarithromycin remain the drugs of choice in our area.

Central venous catheter-related bacteremia due to Tsukamurella species in the immunocompromised host: a case series and review of the literature.

We report 6 cases of bacteremia due to Tsukamurella species, all of which were in immunosuppressed patients with indwelling central venous catheters (CVCs). Fewer than 20 cases of serious illness due to these gram-positive bacilli have been reported in the medical literature; these cases have mostly been ascribed to the species Tsukamurella paurometabola. Tsukamurella species are frequently misidentified as Rhodococcus or Corynebacterium species. We used high-performance liquid chromatography to identify these organisms to the genus level and 16S ribosomal RNA gene sequencing and DNA-DNA dot blots for species identification. Three of our isolates were identified as Tsukamurella pulmonis, 1 was identified as Tsukamurella tyrosinosolvans, and 1 was identified as a unique species. One isolate was not maintained long enough for species identification. All patients were successfully treated with antimicrobial therapy and CVC removal. Infection with this organism should be considered in the immunosuppressed patient with an indwelling CVC and gram-positive bacilli in the blood.

Clonal analysis of gliomas.

In malignant gliomas, the characteristically heterogeneous features and frequent diffuse spread within the brain have raised the question of whether malignant gliomas arise monoclonally from a single precursor cell or polyclonally from multiple transformed cells forming confluent clones. Although monoclonality has been shown in surgically resected tissues, these may not include the full spectrum of patterns seen on autopsy material. Little is known about the clonality of low-grade gliomas from which malignant gliomas may sometimes arise. We sought to investigate the clonality of low-grade and malignant gliomas by using and comparing surgical and autopsy material with a Polymerase chain reaction (PCR)-based assay for nonrandom X chromosome inactivation. For that, purpose, archival surgical and autopsy material from 15 female patients (group A) (age 4 to 73 years; median, 45) with malignant gliomas (12 glioblastomas, one gliosarcoma, one anaplastic oligoastrocytoma, one gliomatosis cerebri), surgical material only from 21 female patients (group S) (age 6 to 78 years; median, 60) with low-grade and malignant gliomas (four low-grade astrocytomas, three oligoastrocytomas, two anaplastic astrocytomas, one gemistocytic astrocytoma, four oligodendrogliomas, seven glioblastomas) were analyzed. In group A, representative areas (mean = 5/patient; median = 7) were microdissected from tissue sections and assayed by PCR amplification of a highly polymorphic microsatellite marker locus of the human androgen receptor gene (HUMARA) in the presence of alpha32P with and without predigestion with a methylation-sensitive restriction enzyme (HhaI). Products were resolved by denaturing gel electrophoresis and autoradiographed. In group S, selected tumor areas were used for the assay. Each patient's normal brain tissue was used for control. The band intensity of alleles were measured by densitometric scanning. In group A, 13 of 15 cases were informative (heterozygous). The same pattern of nonrandom X chromosome inactivation was present in all areas of solid dense and moderate tumor infiltration in eight including all components of the gliosarcoma. Two of eight also showed focal loss of heterozygosity (LOH). One of 13 presented global LOH. Two of 13 showed microsatellite instability, one of which in a patient with Turcot syndrome, the other in gliomatosis cerebri. Opposite skewing patterns were seen in distant areas of gliomatosis cerebri consistent with oligoclonal derivation. Clonality remained indeterminate in one glioblastoma and in the anaplastic oligoastrocytoma because of skewed lyonization in the normal control. In group S, 19 of 21 cases were informative. Fifteen of 19 were monoclonal (four low-grade astrocytomas, one anaplastic astrocytoma, one gemistocytic astrocytoma, two oligodendrogliomas, one oligoastrocytoma, six glioblastomas). Four of 19 were indeterminate. We conclude that (1) Low-grade and malignant gliomas are usually monoclonal tumors, and extensively infiltrating tumors must result from migration of tumor cells (2) Gliomatosis cerebri may initiate as an oligoclonal process or result from collision gliomas (3) Biphasic gliomas likely arise from a single precursor cell. (4) LOH at the HUMARA locus is probably related to partial or complete deletion of an X-chromosome, which occurs in malignant gliomas during clonal evolution.

Chromosomal analysis of renal angiomyolipoma by comparative genomic hybridization: evidence for clonal origin.

Angiomyolipoma has long been considered a hamartomatous polyclonal proliferation. However, recent molecular analyses have indicated that these tumors may be clonal neoplasms rather than polyclonal proliferations. We investigated chromosomal imbalances in angiomyolipoma by comparative genomic hybridization. DNA was extracted from archival paraffin-embedded and frozen tissues of 12 angiomyolipomas (10 usual variant, two epithelioid variant). The 10 angiomyolipomas of the usual variant included bilateral tumors from one tuberous sclerosis patient. Fluorescence ratio distributions from tumor hybridizations were compared with those from control hybridizations to detect changes in DNA copy number with high sensitivity and specificity. We identified 20 chromosomal imbalances in seven sporadic angiomyolipomas, including both tumors of the epithelioid variant. The remaining five tumors, including the two angiomyolipomas from a tuberous sclerosis patient, were devoid of chromosomal imbalances. Seventy-five percent of the imbalances were partial or whole chromosomal deletions involving disparate genomic regions, some of which have previously been associated with tumors of adipose tissue and smooth muscle tumors. Four angiomyolipomas of the usual variant showed 5q deletions with a common region of deletion spanning 5q33 to q34. In two tumors, deletion on 5q was the sole abnormality. One epithelioid angiomyolipoma showed 5q gain encompassing the same region in addition to other alterations. We concluded that (1) Chromosomal imbalances are common in renal angiomyolipomas; (2) Presence of clonal genomic alterations lends further support to the neoplastic pathogenesis of these tumors; (3) The 5q33-q34 region may contain a tumor suppressor gene significant in the histogenesis of some renal angiomyolipomas.

Fatal brain infection caused by Aspergillus glaucus in an immunocompetent patient identified by sequencing of the ribosomal 18S-28S internal transcribed spacer.

Cerebral aspergillosis has rarely been reported in immunocompetent patients. We herein describe a unique case of cerebral aspergillosis in a healthy adult that led to his death despite aggressive antifungal therapy. Sequencing of ribosomal 18S-28S internal transcribed spacer identified the organism as Eurotium herbariorum, the teleomorph of Aspergillus glaucus.

Pediatric renal carcinoma associated with Xp11.2 translocations/TFE3 gene fusions and clinicopathologic associations.

Renal cell carcinomas (RCCs) are rare in children and studies of their subtypes and clinicopathologic associations are limited to small series. We identified 8 patients with RCC treated at our institution between 1981 and 2003, reviewed their clinicopathologic features, cytogenetics findings, and evaluated the status of TFE3 expression by immunohistochemistry and numerical chromosomal alterations by interphase fluorescent in situ hybridization on paraffin-embedded tissue. These 8 patients (5 female and 3 male) had diploidy, and 5 had morphologic features compatible with the recently described RCC associated with Xp11.2 translocations/TFE3 gene fusions and demonstrated nuclear labeling for TFE3 protein by immunohistochemistry. The translocation was confirmed in 2 of these 5 patients by conventional cytogenetics. One case was a high-grade nonpapillary RCC and the other was compatible with type 2 papillary RCC. Four patients showed at least 1 chromosomal gain including trisomy 7 and/or trisomy 17. None of the tumors from male patients showed evidence of loss of the Y chromosome, but 2 patients showed numerical abnormalities of X chromosome +add(X). Two patients had sickle cell disease, and 1 of these also had stage IV-S neuroblastoma. This study suggests that many cases of RCC in children reported under the terms "papillary" and "clear cell" likely represent Xp11.2 translocation/TFE3 gene fusion-associated RCC. It also emphasizes the unusual associations of RCC with neuroblastoma and sickle cell hemoglobinopathy, which need further study.

Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA genes.

Identification of medically relevant yeasts can be time-consuming and inaccurate with current methods. We evaluated PCR-based detection of sequence polymorphisms in the internal transcribed spacer 2 (ITS2) region of the rRNA genes as a means of fungal identification. Clinical isolates (401), reference strains (6), and type strains (27), representing 34 species of yeasts were examined. The length of PCR-amplified ITS2 region DNA was determined with single-base precision in less than 30 min by using automated capillary electrophoresis. Unique, species-specific PCR products ranging from 237 to 429 bp were obtained from 92% of the clinical isolates. The remaining 8%, divided into groups with ITS2 regions which differed by /=99%. Seven clinical isolates contained ITS2 sequences that did not agree with their phenotypic identification, and ITS2-based phylogenetic analyses indicate the possibility of new or clinically unusual species in the Rhodotorula and Candida genera. This work establishes an initial database, validated with over 400 clinical isolates, of ITS2 length and sequence polymorphisms for 34 species of yeasts. We conclude that size and restriction analysis of PCR-amplified ITS2 region DNA is a rapid and reliable method to identify clinically significant yeasts, including potentially new or emerging pathogenic species.

Clinicopathologic and interphase cytogenetic analysis of papillary (chromophilic) renal cell carcinoma.

Trisomy 7 and 17 with deletion of Y is typical of papillary renal cell adenoma (PRCA), and additional alterations occur in the putative genetic progression toward papillary renal cell carcinoma (PRCC). Our study correlated aneuploidy with clinicopathologic features in PRCCs. We used fluorescence in situ hybridization to assess copy number for chromosomes 7, 8, 10, 12, 16, 17, and Y in 16 PRCCs and surrounding benign tubular parenchyma from 15 patients by use of alpha satellite (centromere) probes on deparaffinized tissue sections. We then compared the pattern of monosomy/nullisomy or trisomy/polysomy/hemidisomy to clinicopathologic parameters. Nine tumors (58% Group 1) showed the numeric aberrations typical of PRCAs and PRCCs, with gains of 7 and 17 and loss of Y. We also identified four trisomies of 12 and 16 and one of 8 in Group 1. The remaining seven cases (Group 2) were cytogenetically atypical. Two displayed borderline loss of chromosome 7, although trisomy 17 was present in both. Five had trisomy 7, but none exhibited chromosome 17 alterations, and two exhibited a gain of Y. Neoplasms in Group 2 were less often multicentric than were Group 1 tumors, and they contained foamy macrophage infiltrates less often. One chromophilic carcinoma with abundant clear cells and another with oncocytic features exhibited Group 2 chromosomal profiles. One patient (nuclear grade 4) died from disease, and 14 had no evidence of carcinoma at the last follow-up. We concluded that PRCCs represent a histologically and genotypically heterogeneous group of tumors. If PRCAs consistently exhibit +7, +17, and -Y, it is uncertain whether PRCCs always evolve directly from such lesions. The presence of genotypic heterogeneity might reflect histologic variants of PRCCs, which overlap with other types of RCC. PRCC is generally an indolent neoplasm, despite a high frequency of chromosomal aneuploidy.

Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts.

Species-specific polymorphisms in the noncoding internal transcribed spacer 2 (ITS2) region of the rRNA operon provide accurate identification of clinically significant yeasts. In this study, we tested the hypothesis that ITS1 noncoding regions contain diagnostically useful alleles. The length of ITS1 region PCR products amplified from 40 species (106 clinical strains, 5 reference strains, and 30 type strains) was rapidly determined with single-base precision by automated capillary electrophoresis. Polymorphisms in the PCR product length permitted 19 species to be distinguished by ITS1 alone, compared with 16 species distinguished by using only ITS2. However, combination of both ITS alleles permitted identification of 30 species (98% of clinical isolates). The remaining 10 species with PCR products of similar sizes contained unique ITS alleles distinguishable by restriction enzyme analysis. DNA sequence analysis of amplified ITS1 region DNA from 79 isolates revealed species-specific ITS1 alleles for each of the 40 pathogenic species examined. This provided identification of unusual clinical isolates, and 53 diagnostic ITS1 sequences were deposited in GenBank. Phylogenetic analyses based on ITS sequences showed a similar overall topology to 26S rRNA gene-based trees. However, different species with identical 26S sequences contained distinct ITS alleles that provided species identification with strong statistical support. Together, these data indicate that the analysis of ITS polymorphisms can reliably identify 40 species of clinically significant yeasts and that the capacity for identifying potentially new pathogenic species by using this database holds significant promise.

Application of 16S rRNA gene sequencing to identify Bordetella hinzii as the causative agent of fatal septicemia.

We report on the first case of fatal septicemia caused by Bordetella hinzii. The causative organism exhibited a biochemical profile identical to that of Bordetella avium with three commercial identification systems (API 20E, API 20 NE, and Vitek GNI+ card). However, its cellular fatty acid profile was not typical for either B. avium or previously reported strains of B. hinzii. Presumptive identification of the patient's isolate was accomplished by traditional biochemical testing, and definitive identification was achieved by 16S rRNA gene sequence analysis. Phenotypic features useful in distinguishing B. hinzii from B. avium were production of alkali from malonate and resistance to several antimicrobial agents.

Tsukamurella strandjordae sp. nov., a proposed new species causing sepsis.

We have isolated a gram-positive, weakly acid-alcohol-fast, irregular rod-shaped bacterium from cultures of blood from a 5-year-old girl with acute myelogenous leukemia. This isolate was compared with 14 other strains including reference strains of Tsukamurella species by a polyphasic approach based on physiological and biochemical properties, whole-cell short-chain fatty acid and mycolic acid analyses, DNA-DNA hybridization, and sequencing of the 16S rRNA gene. This isolate represents a new taxon within the genus Tsukamurella for which we propose the name Tsukamurella strandjordae sp. nov. Our study also revealed that Tsukamurella paurometabola ATCC 25938 represents a misnamed Tsukamurella inchonensis isolate and confirms that Tsukamurella wratislaviensis belongs to the genus Rhodococcus.