Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice

BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale

Characterization of bla(OXA-143) Variants in Acinetobacter baumannii and Acinetobacter pittii

The acquired carbapenem- hydrolyzing oxacillinase ( OXA) OXA- 143 has thus far been detected only in Acinetobacter baumannii isolates from Brazil. The aim of this study was to characterize three OXA- 143 variants: OXA- 231 and OXA- 253 from carbapenem-resistant A. baumannii isolates and OXA- 255 in a carbapenem- susceptible Acinetobacter pittii isolate originating from Brazil, Honduras, and the United States, respectively. The 5' rapid amplification of cDNA ends ( RACE) technique identified the same transcription initiation site for all bla(OXA-143-like) genes and revealed differences in the putative promoter regions. However, all cloned OXA- 143 variants conferred carbapenem resistance on A. baumannii ATCC 17978 and OXA- 255 conferred carbapenem resistance on A. pittii SH024, which was correlated with blaOXA- 255 gene expression. This is the first description of OXA- 143- like outside A. baumannii. Detection of OXA- 143- like in the United States and Honduras indicates its dissemination through the American continent

Non–carbapenemase-producing <i>enterobacteriaceae</i> subjected to the CIM method, compared to the CarbaNP test.

<p>Non–carbapenemase-producing <i>enterobacteriaceae</i> subjected to the CIM method, compared to the CarbaNP test.</p

The avian fli gene is specifically expressed during embryogenesis in a subset of neural crest cells giving rise to mesenchyme

The ets-family of transcription factors is involved in the development of endothelial and hematopoietic cells. Among these genes, fli was shown to be responsible for erythroblastomas and Ewing's sarcomas. Its involvement in Ewing's sarcoma, a putative neurectodermal tumor, as well as the in situ hybridization studies performed in mice and Xenopus suggested a role in neural crest development. We cloned quail iii cDNA in order to analyze in more detail its expression in neural crest cells, which have been extensively studied in avian species. Fli gene maps on chicken chromosome 1 to band q31-->q33. Two RNAs are transcribed, most likely arising from two different promoters. The analysis of its expression in neural crest cells reveals that it is expressed rather late, when the neural crest cells reach their target. Among the various lineages derived from the crest, it is restricted to the mesenchymal one. It is maintained at later stages in the cartilage of neural crest but also of mesodermal origin. In addition, iii is expressed in several mesoderm-derived cells: endothelial cells as well as intermediate and splanchnopleural mesoderm

Draft Genome Sequence of NDM-1-Producing Leclercia adecarboxylata

Here, we provide the first draft genome sequence of NDM-1-producing Leclercia adecarboxylata, a human-opportunistic pathogen. The draft genome sequence consists of a total length of 5.13 Mbp, with an average G+C content of 55.2%

Characterization of novel VIM carbapenemase, VIM-38, and first detection of GES-5 carbapenem-hydrolyzing beta-lactamases in Pseudomonas aeruginosa in Turkey

Pseudomonas aeruginosa isolates were collected form a Turkish hospital. Antimicrobial susceptibility was performed using the Vitek 2 Compact system, and 24 isolates were categorized as multidrug resistant (n = 18), extensively-drug resistant (n = 5), or pan-drug resistant (n = I). PCR and DNA sequence analysis revealed that 1 strain possessed the bla(GES-5) and another carried a novel bla(VIM) variant, named VIM-38. This new gene exhibited 1 amino acid substitution (Ala265Val) in comparison to its closest variant, VIM-5. Both VIM encoding genes were clones and demonstrated similar susceptibility profile when expressed in identical background. The presence of VIM-38 increases the diversity of carbapenemases in Turkey. (C) 2014 Elsevier Inc. All rights reserved.This work was supported by Recep Tayyip Erdogan University Research Fund Grants BAP-2012.106.01.11 and BAP-2011.102.03.3

Genetic and Biochemical characterization of OXA-519, a novel OXA-48-like β-lactamase.

A multidrug-resistant 1210 isolate with reduced carbapenem susceptibility revealed the presence of a novel plasmid-encoded gene, named The 60.7-kb plasmid (pOXA-519) was similar to the IncL-OXA-48 prototypical plasmid except for a ca. 2-kb deletion due to an IS insertion. OXA-519 differed from OXA-48 by a Val120Leu substitution, which resulted in an overall reduced ß-lactam-hydrolysis profile, except for ertapenem and meropenem that was increased. Thus, detection of OXA-519-producers using biochemical tests monitoring imipenem-hydrolysis will be difficult

Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant.

OXA-48-producing Enterobacterales have now widely disseminated throughout the world. Several variants have now been reported, differing by just a few amino-acid substitutions or deletions, mostly in the region of the loop β5-β6. As OXA-48 hydrolyzes carbapenems but lacks significant expanded-spectrum cephalosporin (ESC) hydrolytic activity, ESCs were suggested as a therapeutic option. Here, we have characterized OXA-517, a natural variant of OXA-48- with an Arg214Lys substitution and a deletion of Ile215 and Glu216 in the β5-β6 loop, capable of hydrolyzing at the same time ESC and carbapenems. MICs values of E. coli expressing gene revealed reduced susceptibility to carbapenems (similarly to OXA-48) and resistance to ESCs. Steady-state kinetic parameters revealed high catalytic efficiencies for ESCs and carbapenems. The gene was located on a ca. 31-kb plasmid identical to the prototypical IncL -carrying plasmid except for an IS-mediated deletion of 30.7-kb in the operon. The crystal structure of OXA-517, determined to 1.86 Å resolution, revealed an expanded active site compared to that of OXA-48, which allows for accommodation of the bulky ceftazidime substrate. Our work illustrates the remarkable propensity of OXA-48-like carbapenemases to evolve through mutation/deletion in the β5-β6 loop to extend its hydrolysis profile to encompass most β-lactam substrates