Characterization of epidemic IncI1-Iγ plasmids harboring ambler class A and C genes in Escherichia coli and Salmonella enterica from animals and humans

The aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained from Escherichia coli and Salmonella enterica isolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation in traY and excA genes found in IncI1-Iγ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.

Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station

A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

Biological and pathological features in pregnancy-associated breast cancer: a matched case-control study

BACKGROUND

The prognosis for breast cancer has been considered to be worsened by the coexistence of pregnancy. However, to date, significant controversy still exists regarding the pathological tumor features and prognosis of patients diagnosed with pregnancy-associated breast cancer (PABC). The aim of the present study was to analyze the different prognostic factors and outcome in PABC subset versus a non-PABC control group matched for age and year of diagnosis.

MATERIALS AND METHODS

A total of 56 PABC cases were diagnosed from 1990 to 2008, for whom 73 non-PABC patients were identified. Pathological characteristics, immunohistochemical fea- tures, and differences in overall and disease-free survival were compared between both groups.

RESULTS

Compared to non-PABC controls, PABC patients presented more advanced disease (31% vs 13%, p = 0.024) and greater lymph node involvement (53% vs 34%, p = 0.034). Pathological and tumor features tended to present poorer prognostic factors in the PABC subset. Survival was poorer in the PABC patients (five-year DFS 68% in PABC vs 86% in non-PABC, p = 0.12). However, analysing survival adjusted for stage and age, the authors did not find significant differences between both groups.

CONCLUSIONS

PABC patients tended to be diagnosed in advanced breast disease and presented tumors with adverse pathological prognostic factors. While the authors found a poorer outcome in PABC group, no significant differences were observed with stage-matched analysis. The present results may suggest that the poorer prognosis observed within PABC women could not be due to pregnancy itself, but with a delay in diagnosis and tumor subtype pathological features.

Precision Measurement of the (e^{+}+e^{-}) Flux in Primary Cosmic Rays from 0.5 GeV to 1 TeV with the Alpha Magnetic Spectrometer on the International Space Station

We present a measurement of the cosmic ray (e^{+}+e^{-}) flux in the range 0.5 GeV to 1 TeV based on the analysis of 10.6 million (e^{+}+e^{-}) events collected by AMS. The statistics and the resolution of AMS provide a precision measurement of the flux. The flux is smooth and reveals new and distinct information. Above 30.2 GeV, the flux can be described by a single power law with a spectral index γ=-3.170±0.008(stat+syst)±0.008(energy scale).

Hormone receptor and HER2 status: The only predictive factors of response to neoadjuvant chemotherapy in breast cancer

We report our experience in neoadjuvant breast cancer chemotherapy in a single centre between 2000 and 2011. We looked for predictive factors for response to neoadjuvant chemotherapy in the present study. A total of 110 consecutive breast cancer patients were treated with neoadjuvant chemotherapy in our centre. Pathological response was achieved in 24 HR+/HER2- (38.7%), 25 HER2+ (67.6%) and five triple-negative (45.5%) (p = 0.02) patients. No statistically significant differences were found in pathological tumour response according to T stage. The multivariate analysis revealed tumour subtype was the only associated factor for pathological response, with HER2 + tumours the best responders, OR 3.9 (1.5-9.9): 5-year DFS was 40% HER2+/no response; 78% HER2+/response; 65% HR+/HER2-/no response; 82% HR+/HER2-/response; 25% triple-negative/no response and 100% triple-negative/response. HR and HER2 status were the only prognostic factors for pathological response. pCR was correlated with survival in all tumour subtypes.

Treatment of a wastewater from a pesticide manufacture by combined coagulation and Fenton oxidation

The treatment of a non-biodegradable agrochemical wastewater has been studied by coupling of preliminary coagulation-flocculation step and further Fenton oxidation. High percentages of chemical oxygen demand (COD) removal (up to 58 %) were achieved in a first step using polyferric chloride as coagulant. This reduced significantly the amount of H2O2 required in the further Fenton oxidation. Using the stoichiometric amount relative to COD around 80 % of the remaining organic load was mineralized. The combined treatment allowed achieving the regional discharge limits of ecotoxicity at a cost substantially lower than the solution used so far where these wastewaters are managed as hazardous wastes.

Electron and positron fluxes in primary cosmic rays measured with the alpha magnetic spectrometer on the international space station

Precision measurements by the Alpha Magnetic Spectrometer on the International Space Station of the primary cosmic-ray electron flux in the range 0.5 to 700 GeV and the positron flux in the range 0.5 to 500 GeV are presented. The electron flux and the positron flux each require a description beyond a single power-law spectrum. Both the electron flux and the positron flux change their behavior at ∼30  GeV but the fluxes are significantly different in their magnitude and energy dependence. Between 20 and 200 GeV the positron spectral index is significantly harder than the electron spectral index. The determination of the differing behavior of the spectral indices versus energy is a new observation and provides important information on the origins of cosmic-ray electrons and positrons.

High statistics measurement of the positron fraction in primary cosmic rays of 0.5-500 GeV with the alpha magnetic spectrometer on the international space station

A precision measurement by AMS of the positron fraction in primary cosmic rays in the energy range from 0.5 to 500 GeV based on 10.9 million positron and electron events is presented. This measurement extends the energy range of our previous observation and increases its precision. The new results show, for the first time, that above ∼200  GeV the positron fraction no longer exhibits an increase with energy.

Variability in chemical composition of Vitis vinifera cv Mencía from different geographic areas and vintages in Ribeira Sacra (NW Spain)

A chemical study was conducted from 2009 to 2012 to examine spatial and seasonal variability of red Vitis vinifera Mencía located in different geographic areas (Amandi, Chantada, Quiroga-Bibei, Ribeiras do Sil and Ribeiras do Miño) from NW Spain. Mencía samples were analysed for phenolic, (flavan-3-ols, flavonols, anthocyanins, acids and resveratrol), nitrogen (TAC, TAN, YAN and TAS) and volatiles compounds (alcohols, C6 compounds, ethyl esters, terpenes, aldehydes, acids, lactones, volatile phenols and carbonyl compounds) by GC-MS and HPLC. Results showed that the composition of Mencía cultivar was more affected by the vintage than the geographic area. The amino acid composition was less affected by both geographic origin and vintage, showing more varietal stability. Application of Principal Component Analysis (PCA) to experimental data showed a good separation of Mencía grape according to geographical origin and vintages. PCA also showed high correlations between the ripening ratio and C6 compounds, resveratrol and carbonyl compounds.

Chromosomal location of blaCTX-M genes in clinical isolates of Escherichia coli from Germany, The Netherlands and the UK

This study aimed to detect and characterise clinical Escherichia coli isolates suspected of carrying chromosomally encoded CTX-M enzymes. Escherichia coli (n=356) obtained in Germany, The Netherlands and the UK (2005-2009) and resistant to third-generation cephalosporins were analysed for the presence of ESBL-/AmpC-encoding genes within the European SAFEFOODERA-ESBL project. β-Lactamases and their association with IS26 and ISEcp1 were investigated by PCR. Isolates were typed by phylogenetic grouping, MLST and PFGE. Plasmids were visualised by S1 nuclease PFGE, and the location of blaCTX-M genes was determined by Southern hybridisation of XbaI-, S1- and I-CeuI-digested DNA. ESBL enzymes could not be located on plasmids in 17/356 isolates (4.8%). These 17 isolates, from different countries and years, were ascribed to phylogenetic groups D (9), B2 (6) and B1 (2), and to seven sequence types, with ST38 being the most frequent (7 phylogroup D isolates). Eleven isolates produced CTX-M-15. blaCTX-M-15 genes were associated with ISEcp1. The remaining isolates expressed the CTX-M group 9 β-lactamases CTX-M-14 (4), CTX-M-9 (1) and CTX-M-51 (1). blaCTX-M probes hybridised with I-CeuI- and/or XbaI-digested DNA, but not with S1-digested DNA, corroborating their chromosomal location. To summarise, only 4.8% of a large collection of ESBL-producing E. coli isolates harboured chromosomal blaCTX-M genes. These isolates were of human origin and belonged predominantly to ST38 and ST131, which possibly indicates the role of these sequence types in this phenomenon. However, heterogeneity among isolates was found, suggesting that their spread is not only due to the dispersion of successful E. coli clones.

Association of matrix Gla protein gene functional polymorphisms with loss of bone mineral density and progression of aortic calcification

Two matrix Gla protein (MGP) polymorphisms were associated with progression of aortic calcification and femoral neck bone loss in men. All these findings were also functionally corroborated in two vascular and bone in vitro systems indicating that MGP genetic variations can be partly responsible of higher risk of bone loss and vascular calcification.

INTRODUCTION

MGP plays an important role in bone and vascular mineralization as confirmed by MGP-deficient murine model. We therefore aimed to find a genetic association among -138T>C, -7G>A, and Thr83Ala MGP single-nucleotide polymorphisms (SNPs), bone loss, and progression of aortic calcification in a randomly selected general population of 296 individuals who participated in the European Vertebral Osteoporosis Study.

METHODS

To evaluate the rate of change in bone mineral density (BMD) and the progression of aortic calcification, dual X-ray absorptiometry and lateral spine X-rays were performed at baseline and after 4 years of follow-up. Genotyping for the three polymorphisms was carried out using polymerase chain reaction and restriction fragment length analysis. In addition, functional studies of MGP-7G>A and Thr83Ala SNPs were performed on transiently transfected osteoblast-like UMR-106 and vascular smooth muscle A7r5 cells.

RESULTS

The proportion of men who had lost BMD in the femoral neck was higher among homozygous -7AA and 83Ala-Ala (p = 0.039 and p = 0.009, respectively), and also featured a higher risk of progression of aortic calcifications (OR = 5.6, 95% CI = 1.2-27.8 and OR = 6.8, 95% CI = 1.4-32.3, respectively). No effect was observed in women. The MGP-7A allele produced a reduction in luciferase activity compared to MGP-7G: 47% less in vascular cells and 34% less in bone cells (p = 0.001 and 0.012, respectively). In vascular cells under calcifying conditions, the MGP 83Thr allele showed a slightly higher, although not significant, inhibition than the MGP 83 Ala allele in calcium content suggesting functional differences between both variants.

CONCLUSION

These results suggest that MGP genetic variations could predict a higher risk of bone loss and progression of vascular calcification in men.

Isolation of Mycoplasma genitalium from patients with urogenital infections: first report from the Latin-American region

Isolation of Mycoplasma genitalium from clinical specimens remains difficult. We describe a modified culture system based on Vero cells grown in medium 199 with 2% foetal bovine serum (FBS). The culture system was evaluated using early passage M. genitalium strains M6271 and M6311 with growth monitoring by quantitative TaqMan PCR. Eleven endocervical swabs and one male urethral swab positive by 16S rRNA and MgPa1–3 PCRs were quantified and inoculated into Vero cell suspensions in medium 199 supplemented with 2% FBS and antibiotics. Cultures were incubated for 14 days. Cell passages and growth monitoring by TaqMan PCR were performed until the growth of M. genitalium reached ≥10⁶ geq/mL. Confirmation of the new M. genitalium strains was performed by sequencing a 281 bp fragment of mgpB. The growth of Mycoplasma genitalium strains was recorded for all urogenital swab specimens in the modified cell-culture system. Growth of M. genitalium was obtained within 2 months and yielded 12 M. genitalium strains with all 11 isolates from females of an identical, but unique genotype. To our knowledge, this is the first successful isolation of M. genitalium in the Latin-American region. The use of Vero cell culture in 199 medium with 2% FBS is a method comparable to the Ultroser G culture system for isolation of M. genitalium. Genotyping of clinical samples and isolates should be performed to document the absence of cross-contamination.

Liquid chromatography quadrupole time-of-flight mass spectrometry quantification and screening of organophosphate compounds in sludge

For the first time, we assess the performance of liquid chromatography (LC) quadrupole time-of-flight (QTOF) mass spectrometry (MS) for the selective quantification of eight organophosphate compounds (OPs), used as plasticizers and flame retardants additives, in sludge from urban sewage treatment plants (STPs). Moreover, the usefulness of accurate, full scan MS and MS/MS spectra to screen and to confirm the presence of additional OPs, without using reference standards, in sludge samples is discussed. Matrix solid-phase dispersion (MSPD) was used as a sample preparation technique. Under optimized conditions, MSPD provided quantitative recoveries for the group of targeted analytes, requiring just 15 mL of solvent and integrating extraction and clean-up processes in the same step. For these species, the achieved limits of quantification (LOQs) varied between 2 and 50 ng g(-1) and the efficiency of electrospray ionization (ESI) did not change significantly between pure standards and sludge extracts. Among targeted OPs, tri(chloroisopropyl) phosphate (TCPP), tributoxyethyl phosphate (TBEP) and triphenyl phosphate (TPP) were ubiquitous in sludge. The average concentrations of TCPP and TBEP stayed above 700 ng g(-1), whereas the mean value for TPP was 67 ng g(-1). Full scan, accurate spectra provided relevant clues for the screening of additional OPs, using a database containing just their empirical formulae and exact molecular weights; however, the occurrence of in-source fragmentation processes hampered the detection and correct identification of those species which did not render the expected [M+H](+) molecular ion, as was the case of 2-ethylhexyl-diphenyl phosphate (EHDPP).