Evaluation of the EntericBio CPE assay for the detection of carbapenemase-producing organisms.

Carbapenemase-producing organisms (CPOs) represent an increasing threat in healthcare facilities and detection of these organisms in the diagnostic laboratory can be challenging. The EntericBio CPE (EBCPE) real-time PCR assay (Serosep Ltd) was evaluated for the detection of NDM, KPC, OXA-48-like, VIM, IMP and GES carbapenemase genes from a panel of 145 multidrug-resistant organisms (29 NDM, 35 OXA-48, 21 VIM, 4 OXA-23, 3 KPC, 5 NDM+OXA-48, 3 GES-5, 1 OXA-23+NDM, 1 IMI, 2 IMP-1 and 41 multidrug-resistant carbapenemase-negative isolates). The EBCPE assay performed well, with 100 % sensitivity and specificity for the detection of all genotypes included in the assay. Turnaround time and laboratory workflow were improved compared to culture-based assays. Users must remain aware of the limitations of molecular assays for CPO detection to ensure implementation of the most suitable CPO diagnostic pathways.

Improving the detection of carbapenemase-producing organisms (CPO) in a low-prevalence setting: evaluation of four commercial methods and implementation of an algorithm of testing.

PURPOSE: Carbapenemase-producing organisms (CPOs) can be resistant to almost all ß-lactams and represent an increasing threat in healthcare facilities. Detection of these organisms in routine diagnostic laboratories is difficult; here we evaluate four commercially available CPO detection assays and assess their suitability for the clinical laboratory. METHODOLOGY: A panel of 95 clinical multidrug-resistant organisms (22 NDM, 24 OXA-48, 19 VIM, 4 OXA-23, 3 KPC, 4 NDM+OXA-48, 1 OXA23+NDM, 1 IMI, 1 IMP-1, 9 ESBL, 3 derepressed AmpC and 4 inducible AmpC producers) were tested by the RESIST-3 O.K.N., RapidEC CarbaNP, Acuitas Resistome and Xpert Carba-R assays.Results/Key Findings. The commercial assays performed well, with high sensitivities (96.2-100 %) and specificities (all, 100 %). The RapidEC CarbaNP and Acuitas Resistome were able to detect the broadest range of carbapenemase genotypes. The RESIST-3 O.K.N. and Xpert CarbaR had the shortest turnaround times, whilst the RapidEC CarbaNP was the only assay included in this study that could detect previously undescribed genotypes. CONCLUSION: Using an algorithm of the RapidEC CarbaNP, followed by either the RESIST-3 O.K.N. (Enterobacteriaceae) or the Xpert Carba-R (Pseudomonas aeruginosa and Acinetobacter spp.) on suspect CPOs allowed rapid in-house detection and genotyping of a high proportion of CPOs, reducing turnaround time by up to 7 days.

An evaluation of the performance of the Dynamiker® Fungus (1-3)-ß-D-Glucan Assay to assist in the diagnosis of Pneumocystis pneumonia.

The Dynamiker® Fungus (1-3)-ß-D-Glucan Assay (D-BDG) has recently become available in the Western Hemisphere for the diagnosis of invasive fungal disease (IFD). Evaluations of its performance for Pneumocystis pneumonia (PcP) are limited. A retrospective evaluation of D-BDG diagnosis of PcP was performed (23 PcP cases and 23 controls). Sensitivity and specificity were 87% and 70%, respectively, reducing the positivity threshold to 45 pg/ml increased sensitivity (96%), whereas a threshold of 300 pg/ml increased specificity (96%). The performance of D-BDG for the detection of PcP is comparable to other IFD, but sensitivity is below that required to confidently exclude PcP.

Diagnostic value of fine needle aspirates processed by ThinPrep® for the assessment of axillary lymph node status in patients with invasive carcinoma of the breast.

OBJECTIVE: To evaluate the utility of ThinPrep® as an optional specimen processing method for the detection of axillary lymph node metastasis of invasive breast carcinoma. METHODS: A computer SNOMED search from the file at our institution between January 2003 and August 2011 retrieved a total of 209 fine needle aspiration (FNA) specimens of axillary lymph nodes prepared by ThinPrep and followed by axillary lymph node biopsy and/or dissection. Original cytological diagnoses and corresponding histological diagnoses were documented. Using the histological diagnoses as the gold standard, the diagnostic parameters including sensitivity, specificity, positive (PPV) and negative predictive values (NPV) and diagnostic accuracy were calculated. Both cytology and histology slides from cyto-histologically discrepant cases were reviewed. RESULTS: Out of a total of 209 specimens, 193 (92%) had adequate diagnostic material while the remaining 16 specimens (8%) were inadequate for cytological assessment. The diagnostic specimens included 168 invasive ductal carcinomas (IDC), 15 invasive lobular carcinomas (ILC) and 10 mixed carcinomas (IDC and ILC). Excluding 19 cases with malignant cells on FNA in which no residual tumour was found in fibrotic lymph nodes after neoadjuvant therapy (cytology and histology confirmed on review) ThinPrep detected nodal metastasis with an overall sensitivity of 77.5%, specificity of 100%, PPV of 100% and NPV of 53.7%. Diagnostic accuracy was 82.2%. There was no difference in Bloom-Richardson grade or the number or size of metastases between tumours with true-positive and false-negative cytology. Sampling error was the sole factor contributing to cyto-histological discrepancy. CONCLUSIONS: ThinPrep is a good alternative to the conventional smear for cytological assessment of axillary lymph node status in patients with invasive breast carcinoma, particularly when specimens are collected at remote sites or when cytologists are not available for assistance during FNA.

NPM-ALK signals through glycogen synthase kinase 3ß to promote oncogenesis.

Anaplastic large cell lymphoma (ALCL) is the most common type of pediatric peripheral T-cell lymphoma. In 70-80% of cases, the chromosomal aberration t(2;5)(p23;q35) results in the juxtaposition of anaplastic lymphoma kinase (ALK) with nucleophosmin (NPM) and the subsequent expression of the NPM-ALK fusion protein. NPM-ALK is a chimeric tyrosine kinase, which induces numerous signaling pathways that drive proliferation and abrogate apoptosis. However, the mechanisms that lead to activation of downstream growth regulatory molecules have not been completely elucidated. Using a mass spectrometry-based phosphoproteomic screen, we identified GSK3ß as a signaling mediator of NPM-ALK. Using a selective inhibitor of ALK, we demonstrated that the tyrosine kinase activity of ALK regulates the serine-9 phosphorylation of GSK3ß. Expression of NPM-ALK in 293T cells led to an increase of pS(9)-GSK3ß (glycogen synthase kinase 3 beta) compared with kinase-defective K210R mutant NPM-ALK, but did not affect total GSK3ß levels. Phosphorylation of pS(9)-GSK3ß by NPM-ALK was mediated by the PI3K/AKT signaling pathway. ALK inhibition resulted in degradation of GSK3ß substrates Mcl-1 and CDC25A, which was recovered upon chemical inhibition of the proteasome (MG132). Furthermore, the degradation of Mcl-1 was recoverable with inhibition of GSK3ß. ALK inhibition also resulted in decreased cell viability, which was rescued by GSK3ß inhibition. Furthermore, stable knockdown of GSK3ß conferred resistance to the growth inhibitory effects of ALK inhibition using viability and colony formation assays. pS(9)-GSK3ß and CDC25A were selectively expressed in neoplastic cells of ALK+ALCL tissue biopsies, and showed a significant correlation (P<0.001). Conversely, ALK-ALCL tissue biopsies did not show significant correlation of pS(9)-GSK3ß and CDC25A expression (P<0.2). Our results demonstrate that NPM-ALK regulates the phosphorylation of S(9)-GSK3ß by PI3K/AKT. The subsequent inhibition of GSK3ß activity results in accumulation of CDC25A and Mcl-1, which confers the advantage of growth and protection from apoptosis. These findings provide support for the role of GSK3ß as a mediator of NPM-ALK oncogenesis.

Jacobsen syndrome and Beckwith-Wiedemann syndrome caused by a parental pericentric inversion inv(11)(p15q24).

Here we report on a male infant presenting the typical pattern of Jacobsen syndrome including trigonocephaly, thrombocytopenia, congenital heart defect, urethral stenosis, and partial agenesis of the corpus callosum. Conventional karyotyping, FISH, SKY and CGH analyses showed that the region distal to the MLL locus on 11q23 was lost and replaced by the distal region of 11p, leading to a partial trisomy of 11p and a partial monosomy of 11q. According to ISCN (1995) the karyotype can be described as 46,XY,add(11)(q2?3). ish 11ptel(D11S2071x3),11qtel(VIJyRM2072x1). Array-CGH analysis allowed us to narrow down the breakpoints to 11p15.1 and 11q24.1. Methylation analyses of genes located on 11p showed an increased level of the non-methylated paternal allele of the KCNQ1OT1 gene, confirming the concomitant presence of Beckwith-Wiedemann syndrome (BWS). The phenotype resulting from the 11q deletion seems to dominate the phenotype due to the distal 11p trisomy. Investigation of the parents revealed that this chromosomal rearrangement was caused by a paternal pericentric inversion inv(11)(p15q24). Since chromosomal aberrations like the one described here can easily be overlooked during routine chromosome analysis, combined FISH analysis using subtelomeric and possibly additional probes should be applied if there is any doubt about the integrity of telomeric regions.

M-FISH applications in clinical genetics.

Until recently, presence of de novo marker or derivative chromosomes was quite problematic for genetic counseling especially in prenatal diagnosis, because characterization of marker and derivative chromosomes by conventional cytogenetic techniques was nearly impossible. However, recently developed molecular cytogenetic technique named Multicolor Fluorescence in Situ Hybridization (M-FISH) which paints all human chromosomes in 24 different colors allows us to characterize marker and derivative chromosomes in a single hybridization. In this study, we applied M-FISH to determine the origin of 3 marker and 3 derivative chromosomes. Marker chromosomes were found to originate from chromosome 15 in two postnatal and one prenatal case. Of these, one of the postnatal cases displayed clinical findings of inv dup (115) syndrome and the other of infertility, and the prenatal case went through amniocentesis due to the triple test results. Karyotypes of the patients with derivative chromosomes were designated as 46,XY,der (21)t(1;21)(q32;p11), 46,XX,der(8)t(8;9)(p23;p22) and 46,XX,der(18)t(18;20)(q32;p11.2) according to cytogenetic and M-FISH studies. All of the M-FISH results were confirmed with locus specific or whole chromosome painting probes. The case with der (8)t(8;9) had trisomy 9(p22-pter) and monosomy 8(p23-pter) due to this derivative chromosome. The case with der(18)t(18;20) had trisomy 20(p11.2-pter) and monosomy 18(q32-qter). Parental origins of the derivative chromosomes were analyzed using microsatellite markers located in the trisomic chromosomal segments. Patients' clinical findings were compared with the literature.

Expression of fos and jun genes in human skeletal muscle after exercise.

It is believed that the induction of the fos and jun gene family of transcription factors might be at the origin of genetic events leading to the differential regulation of muscle-specific genes. We have investigated the effect of a 30-min running bout in untrained subjects on the expression of the mRNAs of all members of the fos and jun gene families, including c-fos, fosB, fosBdel, fra-1, and fra-2 as well as c-jun, junB, and junD. While the fos family members were transiently upregulated 10- to 20-fold (an exception being fra-2) the induction of the jun family members was up to 3-fold only. The induction of c-fos could also be demonstrated at the protein level. Both c-fos and c-jun mRNAs were coinduced in muscle fiber nuclei. The induction was not restricted to a particular fiber type, as expected from established muscle fiber recruitment schemes, but followed a "patchy" pattern confined to certain regions of the muscle. The signals leading to the expression of these immediate early genes are therefore unclear.

Identification of novel DNA binding sites recognized by the transcription factor mPOU (POU6F1).

Transcription factors of the POU family recognize DNA through their POU domain which represents a bipartite DNA binding motif consisting of a POU specific domain and a POU homeobox. It is thought that both subdomains make specific contacts with DNA and participate in DNA binding. Here we identify novel DNA binding sites for the POU protein mPOU (POU6F1). The sites contain two TAAT motifs either as palindromes or as direct repeats. DNA binding is mediated through the POU homeobox only. Transactivation experiments revealed that mPOU per se showed no transcriptional activation but could act as a repressor of Oct2A mediated activation.

A human POU domain gene, mPOU, is expressed in developing brain and specific adult tissues.

POU domain genes constitute a family of transcription factors that exhibit distinct temporal and spatial patterns of expression. To investigate the possible functions that POU proteins may have in muscle development we have isolated four novel POU-domain-encoding sequences from human muscle tissue. One of these sequences, referred to as mPOU, encodes a new member of subclass VI of the POU family. In the embryo, mPOU is expressed exclusively in the developing brain, whereas in the adult its expression is restricted to brain, heart, skeletal muscle and lung. In the brain, the highest expression levels were found in specific cell layers of the cortex, the olfactory bulb, the hippocampus and the cerebellum. mPOU is shown to bind to DNA sequences containing the octamer motif and other POU factor target sites. The distinct expression pattern and divergent DNA-binding characteristics indicate that mPOU may regulate a distinct set of genes.

Fast myosin light chain expression in chicken muscles studied by in situ hybridization.

We have studied the fiber type-specific expression of the fast myosin light chain isoforms LC 1f, LC 2f, and LC 3f in adult chicken muscles using in situ hybridization and two-dimensional gel electrophoresis. Type II (fast) fibers contain all three fast myosin light chain mRNAs; Types I and III (slow) fibers lack them. The myosin light chain patterns of two-dimensional gels from microdissected single fibers match their mRNA signals in the in situ hybridizations. The results confirm and extend previous studies on the fiber type-specific distribution of myosin light chains in chicken muscles which used specific antibodies. The quantitative ratios between protein and mRNA content were not the same for all three fast myosin light chains, however. In bulk muscle samples, as well as in single fibers, there was proportionally less LC 3f accumulated for a given mRNA concentration than LC 1f or LC 2f. Moreover, the ratio between LC 3f mRNA and protein was different in samples from muscles, indicating that LC 3f is regulated somewhat differently than LC 1f and LC 2f. In contrast to other in situ hybridization studies on the fiber type-specific localization of muscle protein mRNAs, which reported the RNAs to be located preferentially at the periphery of the fibers, we found all three fast myosin light chain mRNAs quite evenly distributed within the fiber's cross-sections, and also in the few rare fibers which showed hybridization signals several-fold higher than their surrounding counterparts. This could indicate principal differences in the intracellular localization among the mRNAs coding for various myofibrillar protein families.