Effects of UV and Calcium Perchlorates on Uracil Deposited on Strontium Fluoride Substrates at Mars Pressure and Temperature.

Organic matter is actively searched on Mars with current and future space missions as it is a key to detecting potential biosignatures. Given the current harsh environmental conditions at the surface of Mars, many organic compounds might not be preserved over a long period as they are exposed to energetic radiation such as ultraviolet light, which is not filtered above 190 nm by the martian atmosphere. Moreover, the presence of strong oxidizing species in the regolith, such as perchlorate salts, might enhance the photodegradation of organic compounds of astrobiological interest. Because current space instruments analyze samples collected in the upper surface layer, it is necessary to investigate the stability of organic matter at the surface of Mars. Previous experimental studies have shown that uracil, a molecule relevant to astrobiology, is quickly photolyzed when exposed to UV radiation under the temperature and pressure conditions of the martian surface with an experimental quantum efficiency of photodecomposition (φexp) of 0.30 ± 0.26 molecule·photon-1. Moreover, the photolysis of uracil leads to the formation of more stable photoproducts that were identified as uracil dimers. The present work aims to characterize the additional effect of calcium perchlorate detected on Mars on the degradation of uracil. Results show that the presence of calcium perchlorate enhances the photodecomposition of uracil with φexp = 12.3 ± 8.3 molecule·photon-1. Although some of the photoproducts formed during these experiments are common to those formed from pure uracil only, the Fourier transformation infrared (FTIR) detection of previously unseen chemical functions such as alkyne C ≡ C or nitrile C ≡ N has shown that additional chemical species are formed in the presence of calcium perchlorate in the irradiated sample. This implies that the effect of calcium perchlorate on the photolysis of uracil is not only kinetic but also related to the nature of the photoproducts formed.

Past and future of HIV infection. A document based on expert opinion.

HIV infection is now almost 40 years old. In this time, along with the catastrophe and tragedy that it has entailed, it has also represented the capacity of modern society to take on a challenge of this magnitude and to transform an almost uniformly lethal disease into a chronic illness, compatible with a practically normal personal and relationship life. This anniversary seemed an ideal moment to pause and reflect on the future of HIV infection, the challenges that remain to be addressed and the prospects for the immediate future. This reflection has to go beyond merely technical approaches, by specialized professionals, to also address social and ethical aspects. For this reason, the Health Sciences Foundation convened a group of experts in different aspects of this disease to discuss a series of questions that seemed pertinent to all those present. Each question was presented by one of the participants and discussed by the group. The document we offer is the result of this reflection.

BCN Checkpoint: same-day confirmation of reactive HIV rapid test with Point Of Care HIV-RNA accelerates linkage to care and reduces anxiety.

BACKGROUND: The introduction in 2006 of the rapid HIV test by BCN Checkpoint in a non-clinical setting has been a successful step forwards in the uptake of testing. Nevertheless, HIV serostatus should be reported as HIV positive only when a reactive result has been tested again using a different assay (WHO guidelines 2015). The standard confirmation test has been the Western Blot (WB) test. However confirmation results take around 7 days to come back. AIMS: This study explores the possibility of Point of Care PCR testing for a same-day confirmation. MATERIALS AND METHODS: Between March 2015 and September 2016 a POC PCR test (Xpert® HIV-1 Qual) was performed in parallel to the Western Blot test after a reactive HIV rapid test (Alere Determine™ HIV-1/2 Ag/Ab Combo and Alere™ HIV Combo). HIV confirmed positive cases received emotional support by peers, were informed and prepared for treatment initiation and rapidly linked to HIV clinic. RESULTS: During the study period 11 455 tests were performed to 7163 clients. A total of 249 reactive rapid HIV tests were found. For analysis a total of 33 cases were excluded due to the lack of PCR and/or WB test. Results of comparison of the 216 cases showed 194 concordant positive confirmations and 14 concordant negative results. In three cases PCR was positive and WB negative. In five cases PCR was negative and WB positive. CONCLUSION: The POC PCR assay is easy to use and feasible in a community-based center. Reducing time for confirmation to 90 min has been possible in 91.2% (197/216) of cases with positive PCR result. In cases of a negative PCR result an additional test (WB, Elisa or PCR quantitative) was needed to distinguish false positive results (6.5%) from viral load results below level of detection (2.3%). Clients expressed satisfaction with same-day confirmation and less anxiety.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

BACKGROUND: The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. AIMS: The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. SOURCES: Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. CONTENT: Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. IMPLICATIONS: Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner.

Oxidants at the Surface of Mars: A Review in Light of Recent Exploration Results.

In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith. As several exploration missions currently focus on the detection of organics on Mars (or will do so in the near future), knowledge of the oxidative state of the surface is fundamental. It will allow for determination of the capability of organics to survive on a geological timescale, the most favorable places to seek them, and the best methods to process the samples collected at the surface. With this aim, we review the main oxidants assumed to be present on Mars, their possible formation pathways, and those laboratory studies in which their reactivity with organics under Mars-like conditions has been evaluated. Among the oxidants assumed to be present on Mars, only four have been detected so far: perchlorate ions (ClO4-) in salts, hydrogen peroxide (H2O2) in the atmosphere, and clays and metal oxides composing surface minerals. Clays have been suggested as catalysts for the oxidation of organics but are treated as oxidants in the following to keep the structure of this article straightforward. This work provides an insight into the oxidizing potential of the surface of Mars and an estimate of the stability of organic matter in an oxidizing environment. Key Words: Mars surface-Astrobiology-Oxidant-Chemical reactions. Astrobiology 16, 977-996.

Time trends in the aetiology of prosthetic joint infections: a multicentre cohort study.

It is important to know the spectrum of the microbial aetiology of prosthetic joint infections (PJIs) to guide empiric treatment and establish antimicrobial prophylaxis in joint replacements. There are no available data based on large contemporary patient cohorts. We sought to characterize the causative pathogens of PJIs and to evaluate trends in the microbial aetiology. We hypothesized that the frequency of antimicrobial-resistant organisms in PJIs has increased in the recent years. We performed a cohort study in 19 hospitals in Spain, from 2003 to 2012. For each 2-year period (2003-2004 to 2011-2012), the incidence of microorganisms causing PJIs and multidrug-resistant bacteria was assessed. Temporal trends over the study period were evaluated. We included 2524 consecutive adult patients with a diagnosis of PJI. A microbiological diagnosis was obtained for 2288 cases (90.6%). Staphylococci were the most common cause of infection (1492, 65.2%). However, a statistically significant rising linear trend was observed for the proportion of infections caused by Gram-negative bacilli, mainly due to the increase in the last 2-year period (25% in 2003-2004, 33.3% in 2011-2012; p 0.024 for trend). No particular species contributed disproportionally to this overall increase. The percentage of multidrug-resistant bacteria PJIs increased from 9.3% in 2003-2004 to 15.8% in 2011-2012 (p 0.008), mainly because of the significant rise in multidrug-resistant Gram-negative bacilli (from 5.3% in 2003-2004 to 8.2% in 2011-2012; p 0.032). The observed trends have important implications for the management of PJIs and prophylaxis in joint replacements.

Organic molecules in the Sheepbed Mudstone, Gale Crater, Mars.

The Sample Analysis at Mars (SAM) instrument on board the Mars Science Laboratory Curiosity rover is designed to conduct inorganic and organic chemical analyses of the atmosphere and the surface regolith and rocks to help evaluate the past and present habitability potential of Mars at Gale Crater. Central to this task is the development of an inventory of any organic molecules present to elucidate processes associated with their origin, diagenesis, concentration, and long-term preservation. This will guide the future search for biosignatures. Here we report the definitive identification of chlorobenzene (150-300 parts per billion by weight (ppbw)) and C2 to C4 dichloroalkanes (up to 70 ppbw) with the SAM gas chromatograph mass spectrometer (GCMS) and detection of chlorobenzene in the direct evolved gas analysis (EGA) mode, in multiple portions of the fines from the Cumberland drill hole in the Sheepbed mudstone at Yellowknife Bay. When combined with GCMS and EGA data from multiple scooped and drilled samples, blank runs, and supporting laboratory analog studies, the elevated levels of chlorobenzene and the dichloroalkanes cannot be solely explained by instrument background sources known to be present in SAM. We conclude that these chlorinated hydrocarbons are the reaction products of Martian chlorine and organic carbon derived from Martian sources (e.g., igneous, hydrothermal, atmospheric, or biological) or exogenous sources such as meteorites, comets, or interplanetary dust particles. KEY POINTS: First in situ evidence of nonterrestrial organics in Martian surface sediments Chlorinated hydrocarbons identified in the Sheepbed mudstone by SAM Organics preserved in sample exposed to ionizing radiation and oxidative condition.

Two unusual hepatitis C virus subtypes, 2j and 2q, in Spain: Identification by nested-PCR and sequencing of a NS5B region.

Many studies have reported the use of the NS5B gene to subtype hepatitis C virus (HCV). Other HCV genes, such as HCV-5' UTR, Core (C) and E1, have also been used. In some studies, NS5B have been used together with 5'-UTR or C genes to improve genotyping results obtained using commercial procedures. Only two studies in Spain have compared molecular techniques versus commercial procedures regarding the efficacy of HCV subtyping. The aim of this study was to determine whether nested PCR and sequencing of a NS5B region was more reliable than commercial procedures to subtype HCV. We analyzed the results of HCV genotyping in [726] serum specimens collected from 2001 to 2013. From 2001 to 2011, we used PCR and INNO-LiPA hybridization or its new version Versant HCV Genotype 2.0 assay (471 samples). From 2012 to 2013, we used nested PCR and sequencing of a NS5B region (255 cases). This method used two pairs of primers to amplify the RNA of the sample converted to DNA by retrotranscription. The amplification product of 270 base pairs was further sequenced. To identify the subtype, the sequences obtained were compared to those in the international database: http://hcv.lanl.gov./content/sequence/, HCV/ToolsOutline.html and Geno2pheno[hcv] http://hcv.bioinf.mpi-inf.mpg.de/index.php. Nested PCR of a NS5B region and sequencing identified all but one subtype (0.4%, 1/255), differentiated all 1a subtypes from 1b subtypes, and characterized all HCV 2-4 subtypes. This approach also distinguished two subtypes, 2j and 2q, that had rarely been detected previously in Spain. However, commercial procedures failed to subtype 12.7% (60/471) of samples and to genotype 0.6% of specimens (3/471). Nested PCR and sequencing of a NS5B region improved the subtyping of HCV in comparison with classical procedures and identified two rare subtypes in Spain: 2j and 2q. However, full length genome sequencing is recommended to confirm HCV 2j and 2q subtypes.

Implication of Candida parapsilosis FKS1 and FKS2 mutations in reduced echinocandin susceptibility.

We evaluated FKS1 and FKS2 mutations in Candida parapsilosis bloodstream isolates and correlated them with the echinocandin MIC values determined by guidelines in CLSI document M27-A3 and the YeastOne panel. All mutations detected were outside hot spot (HS) regions. The F1386S mutation detected in an isolate that was resistant by the YeastOne panel but not by the M27-A3 guidelines might be implicated in echinocandin resistance. Further studies are needed to confirm the implication of the F1386S mutation and to elucidate the capability of the M27-A3 guidelines to detect echinocandin resistance.

Volatile and organic compositions of sedimentary rocks in Yellowknife Bay, Gale crater, Mars.

H2O, CO2, SO2, O2, H2, H2S, HCl, chlorinated hydrocarbons, NO, and other trace gases were evolved during pyrolysis of two mudstone samples acquired by the Curiosity rover at Yellowknife Bay within Gale crater, Mars. H2O/OH-bearing phases included 2:1 phyllosilicate(s), bassanite, akaganeite, and amorphous materials. Thermal decomposition of carbonates and combustion of organic materials are candidate sources for the CO2. Concurrent evolution of O2 and chlorinated hydrocarbons suggests the presence of oxychlorine phase(s). Sulfides are likely sources for sulfur-bearing species. Higher abundances of chlorinated hydrocarbons in the mudstone compared with Rocknest windblown materials previously analyzed by Curiosity suggest that indigenous martian or meteoritic organic carbon sources may be preserved in the mudstone; however, the carbon source for the chlorinated hydrocarbons is not definitively of martian origin.

Volatile, isotope, and organic analysis of martian fines with the Mars Curiosity rover.

Samples from the Rocknest aeolian deposit were heated to ~835°C under helium flow and evolved gases analyzed by Curiosity's Sample Analysis at Mars instrument suite. H2O, SO2, CO2, and O2 were the major gases released. Water abundance (1.5 to 3 weight percent) and release temperature suggest that H2O is bound within an amorphous component of the sample. Decomposition of fine-grained Fe or Mg carbonate is the likely source of much of the evolved CO2. Evolved O2 is coincident with the release of Cl, suggesting that oxygen is produced from thermal decomposition of an oxychloride compound. Elevated δD values are consistent with recent atmospheric exchange. Carbon isotopes indicate multiple carbon sources in the fines. Several simple organic compounds were detected, but they are not definitively martian in origin.

Outbreak of Pseudomonas fluorescens bloodstream infection in a coronary care unit.

An outbreak of Pseudomonas fluorescens infection in six patients in a coronary care unit was associated with a source not previously reported, namely the ice bath used for cardiac output determinations. Outbreaks of pseudobacteraemia caused by P. fluorescens and occasional blood transfusion-associated bloodstream infection (BSI) have been described. However, during the last two decades, two outbreaks of P. fluorescens BSI have been described and this article reports a third. Isolation of P. fluorescens in blood cultures must alert clinicians to the possibility of contamination of infusate, lock solutions or catheter flush.

Evaluation of the VersaTREK system compared to the Bactec MGIT 960 system for first-line drug susceptibility testing of Mycobacterium tuberculosis.

The aim of this study was to evaluate the reliability of the VersaTREK system for Mycobacterium tuberculosis drug susceptibility testing compared with results obtained with the Bactec MGIT 960 system. A total of 67 strains were evaluated. Overall agreement was at 98.5%. Kappa indexes were 1.0 for isoniazid, rifampin, and ethambutol, 0.937 for pyrazinamide, and 0.907 for streptomycin. The VersaTREK system is validated for M. tuberculosis drug susceptibility testing.

Nosocomial outbreak of Blastoschizomyces capitatus associated with contaminated milk in a haematological unit.

In July 2002, Blastoschizomyces capitatus was isolated from four neutropenic patients in a haematology unit. Two patients died due to disseminated infection while the other two had oropharyngeal colonisation. Nosocomial acquisition of the fungus was suspected and epidemiological and environmental studies were undertaken. To determine the potential source for the acquisition of the fungus, epidemiological relationships between the patients were investigated. We performed surveillance cultures on all patients and took environmental cultures of air, inanimate surfaces, food samples, blood products and chemotherapy drugs. No direct contact transmission between patients was found and B. capitatus was isolated only in vacuum flasks used for breakfast milk distribution. All isolates were compared by four independent molecular typing methods: pulsed-field gel electrophoresis, genomic DNA restriction endonuclease analysis, randomly amplified polymorphic DNA, and polymerase chain reaction fingerprinting using a single primer specific for one minisatellite or two microsatellite DNAs. Milk vacuum flasks and clinical strains were genetically indistinguishable by all typing techniques. Milk vacuum flasks were withdrawn from all hospital units and no further B. capitatus infection was detected. Our findings suggest that clonal dissemination of a single strain of B. capitatus from vacuum flasks used for milk distribution was responsible for this nosocomial outbreak in the haematological unit.

Bacterial DNA in the diagnosis of spontaneous bacterial peritonitis.

BACKGROUND: Despite inoculation into blood culture bottles, ascitic fluid culture is negative in 50% of cases of spontaneous bacterial peritonitis (SBP). AIM: To determine whether 16S rDNA gene detection by real-time polymerase chain reaction (PCR) and sequencing increases the efficacy of culture in microbiological diagnosis of spontaneous bacterial peritonitis. METHODS: We prospectively included 55 consecutive spontaneous bacterial peritonitis episodes in cirrhotic patients, 20 cirrhotic patients with sterile ascites and 27 patients with neoplasic ascites. Ascitic fluid was inoculated into blood culture bottles at the bedside and tested for bacterial DNA by real-time PCR and sequencing of 16S rDNA gene. RESULTS: Bacterial DNA was detected in 23/25 (92%) culture-positive SBP, 16/30 (53%) culture-negative SBP (P = 0.002 with respect to culture-positive SBP), 12/20 (60%) sterile ascites (P = 0.01 with respect to culture-positive SBP) and 0/27 neoplasic ascites (P < 0.001 with respect to other groups). Sequencing identified to genus or species level 12 culture-positive SBP, six culture-negative SBP and six sterile ascites. In the remaining cases with positive PCR, sequencing did not yield a definitive bacterial identification. CONCLUSIONS: Bacterial DNA was not detected in almost half the culture-negative spontaneous bacterial peritonitis episodes. Methodology used in the present study did not always allow identification of amplified bacterial DNA.

Multiclonal epidemic of Klebsiella pneumoniae isolates producing DHA-1 in a Spanish hospital.

Between June 2007 and January 2008, 26 Klebsiella pneumoniae isolates carrying bla(DHA-1) on an IncL/M plasmid were obtained from clinical samples at Granollers Hospital, Barcelona, Spain. Three of the isolates also carried a bla(CTX-M-15) gene. The 26 isolates showed 11 pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing showed that PFGE patterns A, B and C belonged to sequence type (ST)17, D to ST13, E to ST427, F and G to ST416, H to ST37, I to ST440, J to ST326, and K to ST428. Results demonstrated the effectiveness of the infection control programme in place at the centre. This study reports the first characterization of STs for bla(DHA-1) -producing K. pneumoniae isolates.

Prevalence of acquired AmpC beta-lactamases in Enterobacteriaceae lacking inducible chromosomal ampC genes at a Spanish hospital from 1999 to 2007.

In 2007, a significant increase in acquired ampC genes in Enterobacteriaceae from 0.06% in 1999 to 1.3% was observed. Proteus mirabilis showed the highest prevalence (0.95%) and CMY-2 was the most prevalent AmpC enzyme (66.7%). Other enzymes such as CMY-4, DHA-1, ACC-1, and three new enzymes called CMY-25, CMY-27 and CMY-40 were detected. Seven out of the 117 isolates (6%) also produced an extended-spectrum beta-lactamase. As acquired AmpC enzymes are likely to become a serious public health issue worldwide, close surveillance is necessary to curb their spread.

Tuberculosis transmission patterns among Spanish-born and foreign-born populations in the city of Barcelona.

During a 2-year period (2003-2004), tuberculosis (TB) transmission in Barcelona and the factors related to transmission among the Spanish- and foreign-born populations were studied by molecular epidemiology. Data were obtained from TB cases and Conventional Contact Tracing registries and genotyping was performed using restriction fragment length polymorphism (RFLP)-IS6110 and MIRU12 as a secondary typing method. Of the 892 TB cases reported, 583 (65.3%) corresponded to Spanish-born and 309 (34.6%) to foreign-born. Six hundred and eighty-seven cases (77%) were confirmed by culture. RFLP typing of 463/687 (67.4%) isolates was performed, revealing 280 (60.5%) unique and 183 (39.5%) shared patterns, which were grouped into 65 clusters. Spanish-born individuals were significantly more clustered than foreign-born individuals (44.6% vs. 28.8%; p 0.016). Clustering in foreign-born individuals was associated with HIV (p 0.051, odds ratio = 3.1, 95% confidence interval 1-10.9) and alcohol abuse (p 0.022), whereas, in the Spanish-born individuals, clustering was associated with age in the range 21-50 years, (p 0.024). Of the total clusters, 36/65 (55.3%) included only Spanish-born patients, whereas 22/65 (33.8%) included individuals from both populations. In mixed clusters, the index case was Spanish-born in 53% and foreign-born in 47%. Among the foreign-born, 2.8% were ill on arrival, 30% developed TB within the first year and 50.3% developed TB within the first 2 years; 58.3% were from South America. In conclusion, half of the foreign-born TB patients developed the disease during the first 2 years after arrival, which, in most cases, was the result of endogenous reactivation. Recent TB transmission among Spanish-born and foreign-born populations, as well as bidirectional transmission between communities, contributed significantly to the burden of TB in Barcelona, suggesting the need to improve Public Health interventions in both populations.

Plasmid-mediated QnrS2 determinant in an Aeromonas caviae isolate recovered from a patient with diarrhoea.

A qnrS2 gene was identified in an Aeromonas caviae isolate (MICs of ciprofloxacin, norfloxacin and ofloxacin >32 mg/L) from a stool sample collected from a patient with gastroenteritis. The analysis of the gyrA and parC genes revealed amino acid substitutions Ser83-Ile and Ser80-Thr, respectively. In addition, five out of 41 nalidixic acid-resistant Aeromonas isolates studied (26 identified as Aeromonas veronii bv sobria and 15 identified as A. caviae) showed ciprofloxacin resistance. The identification of plasmid-mediated qnr genes outside of the Enterobacteriaceae underlines a possible diffusion of these resistance determinants among Gram-negative rods. This emphasizes the importance of monitoring the emergence of these determinants as well as their dissemination among the Aeromonadaceae.

The fate of aerosols on the surface of Titan.

A laboratory study based on the chemical transformation that Titan's aerosol analogues suffer when placed under putative surface conditions of the satellite was performed. In order to understand the role that aqueous ammonia may play on the chemical transformation of atmospheric aerosols once they reach the surface, we synthesized laboratory analogues of Titan's aerosols from an N2 : CH4 (98 : 2) mixture irradiated at low temperatures under a continuous flow regime by a cold plasma discharge of 180 W. The analogues were recovered, partitioned in several 10.0 mg samples and placed inside different ammonia concentrations during 10 weeks at temperatures as low as those reported for Titan's surface. After a derivatization process performed to the aerosols' refractory phase with MTBSTFA in DMF, the products were identified and quantified using a GC-MS system. We found derived residues related to amino acids as well as urea. The simplest amino acids aminoethanoic acid (glycine) and 2-aminopropanoic acid (alanine) as well as diaminomethanal (urea), are found regardless of the ammonia concentration and temperature value to which the aerosol analogues were exposed. Our results have important astrobiological implications to Titan's environment particularly if the existence of the suggested subsurface water-ammonia mixture and its deposition on the satellite's surface is validated.