The noninvasive detection of Helicobacter pylori and its resistance to clarithromycin could revolutionize the management of H. pylori-infected patients by tailoring eradication treatment without any need for endoscopy when histology is not necessary. Several real-time PCR tests performed on stools have been proposed, but their performances were either poor or they were tested on too few patients to be properly evaluated. We conducted a prospective, multicenter study including 1,200 adult patients who were addressed for gastroduodenal endoscopy with gastric biopsies and who were naive for eradication treatment in order to evaluate the performance of the Amplidiag H. pylori+ClariR assay recently developed by Mobidiag (Espoo, Finland). The results of the Amplidiag H. pylori+ClariR assay performed on DNA from stools (automatic extraction with the EasyMag system [bioMérieux]) were compared with those of culture/Etest and quadruplex real-time PCRs performed on two gastric biopsy samples (from the antrum and corpus) to detect the H. pylori glmM gene and mutations in the 23S rRNA genes conferring clarithromycin resistance. The sensitivity and specificity of the detection of H. pylori were 96.3% (95% confidence interval [CI], 92 to 98%) and 98.7% (95% CI, 97 to 99%), respectively. The positive and negative predictive values were evaluated to be 92.2% (95% CI, 92 to 98%) and 99.3% (95% CI, 98 to 99%), respectively. In this cohort, 160 patients (14.7%) were found to be infected (positive by culture and/or PCR). The sensitivity and specificity for detecting resistance to clarithromycin were 100% (95% CI, 88 to 100%) and 98.4% (95% CI, 94 to 99%), respectively.

Fatty acids with conjugated double bonds have attracted great interest because of their reported potent bioactivities. However, there are currently no rapid methods for their structural characterization. We report here a convenient mass spectrometry-based strategy to establish double bond geometry by analysis of collisional dissociation products of cis/trans and trans/cis conjugated linoleic acids (CLAs), as methyl esters, and to distinguish CLAs from homoallylic (methylene-interrupted) fatty acids in a single-stage mass spectrum. A series of CLA standards with double bond positions 6,8; 7,9; 8,10; 9,11; 10,12; 11,13; 12,14; and 13,15, with all four possible geometries (cis/trans; trans/cis; cis/cis; trans/trans) were analyzed. The m/z 54 (1-methyleneimino)-1-ethenylium ion, generated by self-reaction of acetonitrile under chemical ionization conditions, reacts with unsaturated fatty acids to yield an [M + 54]+ ion, which decomposes in the single-stage mass spectrum by loss of neutral methanol to form [M + 54 - 32]+. The ratio of [M + 54]+/[M + 54 - 32]+ in the single-stage mass spectra of CLA isomers is 1 order of magnitude less than for homoallylic diene FAME. Collisional dissociation of the [M + 54]+ ion yields two diagnostic ions that contain the alpha- and omega-carbon atoms and is characteristic of double bond position in the analyte. The fragment vinylic to the trans double bond is significantly more abundant than that for the cis double bond, revealing double bond geometry. The ratio of alpha to we diagnostic ion abundances is >4.8 for cis/trans isomers, <0.5 for trans/cis isomers, and 0.7-3.2 for cis/cis and trans/trans isomers. This method provides a rapid alternative to conventional conjugated fatty acid analysis and, together with complementary elution time information provided by gas chromatography, enables rapid, positive identification of double bond position and geometry in most CLA FAME.

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Modeling of ion motion and experimental investigations of ion excitation in a linear quadrupole trap with a 4% added octopole field are described. The results are compared with those obtained with a conventional round rod set. Motion in the effective potential of the rod set can explain many of the observed phenomena. The frequencies of ion oscillation in the x and y directions shift with amplitude in opposite directions as the amplitudes of oscillation increase. Excitation profiles for ion fragmentation become asymmetric and in some cases show bistable behavior where the amplitude of oscillation suddenly jumps between high and low values with very small changes in excitation frequency. Experiments show these effects. Ions are injected into a linear trap, stored, isolated, excited for MS/MS, and then mass analyzed in a time-of-flight mass analyzer. Frequency shifts between the x and y motions are observed, and in some cases asymmetric excitation profiles and bistable behavior are observed. Higher MS/MS efficiencies are expected when an octopole field is added. MS/MS efficiencies (N 2 collision gas) have been measured for a conventional quadrupole rod set and a linear ion trap with a 4% added octopole field. Efficiencies are chemical compound dependent, but when an octopole field is added, efficiencies can be substantially higher than with a conventional rod set, particularly at pressures of 1.4 ϫ 10 Ϫ4 torr or less. . The most widely discussed distortion is the "stretched" ion trap [2], which has the end cap electrodes moved out so that the distance to the end cap, z 0 , is increased over that of an ideal field, z 0 ϭ r 0 ⁄ ͙ 2, where r 0 is the distance from the center to the ring electrode. It has been argued that the addition of higher order multipole fields of the correct sign to 3-D traps improves MS/MS efficiency [1c, 1f, 2], and allows faster ejection at the stability boundary [2,3], to give higher scan speeds and improved mass resolution.There is increasing interest in using linear quadrupoles as ion traps, both as stand alone mass analyzers with radial [4] or axial [5] ejection, or in combination with other mass analyzers (for a recent review see [6]).There is also interest in trapping and exciting ions for MS/MS at the relatively low pressures typical for operation of the last mass analyzing quadrupole in triple quadrupole systems, ca. 3 ϫ 10 Ϫ5 torr [7]. Addition of higher multipoles to a linear ion trap might be expected to provide benefits similar to those seen with 3-D traps. Douglas and coworkers [8] have shown that an octopole field can be added to a linear quadrupole by using rod sets with rods equally spaced from the central axis but with one pair of rods different in diameter than the other pair, as shown in Figure 1. The electric potential within this rod set is given to a good approximation bywhere x is the distance from the center towards a smaller rod, y is the distance from the center towards a larger rod, r 0 is the distance from the center to any rod, and U and V rf are the amplitudes...

Objectives: To evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens. Methods: This prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods. Results: A total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/ 515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7% e96.5%) and 96.0% (95% CI 95.5%e96.4%), respectively, when compared with culture. Of FA-PP falsenegative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of 1 log 10 in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with 10 6 DNA copies/mL grew significantly in culture. Conclusions: FA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.