Multi-laboratory proficiency testing of clinical cancer genomic profiling by next-generation sequencing

Next-generation sequencing (NGS) enables parallel analysis of multiple genomic targets. The increasing demand for NGS-based multiplexed molecular diagnostics requires standardized protocols and recommendations to ensure reproducibility and accuracy of test results for routine clinical decision making. However, the lack of clinical NGS data from multi-laboratory tests and the absence of inter-laboratory comparisons have hampered the establishment of instructive clinical NGS standards. To fill the gap, we set up Proficiency Testing (PT) for inter-laboratory comparison, in which formalin-fixed paraffin-embedded specimens from eight lung and eight colon cancers were analyzed by 15 European molecular diagnostic laboratories on three different platforms using multiple target enrichment systems. We first performed platform, test, and informatics pipeline validation and conducted sensitivity and specificity analysis by random in silico down-sampling. We then implemented a multi-level filtering strategy based on performance tests of base substitution, replicate runs, and Sanger sequencing verified variants. We finally applied the filter criteria to the NGS data from the respective PT participants and obtained high inter-laboratory agreement. We demonstrated accuracy, scalability, and robustness of NGS by means of PT, serving as a benchmark for detecting clinically actionable molecular alterations in research and diagnostic laboratories. In conclusion, this study strongly highlights the importance of establishing standards for NGS-based testing, particularly when the test results impact on clinical decisions, and systematically provides data sets from multiple different labs to infer such standards.

Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40

Background

Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.

Results

We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).

Conclusion

Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1367-x) contains supplementary material, which is available to authorized users.

Cross-transmission rates of enterococcal isolates among newborns in a neonatal intensive care unit

Enterococci are important pathogens causing nosocomial infections and patients at risk include also premature babies requiring intensive care treatment. Our aim was to assess occurrence and cross transmission rates of enterococci among neonatal patients of a hospital ward during a two months period. Rectal and skin samples were taken between day one and 60 of infants' age. Colonization with various potentially pathogenic bacteria was correlated with developing a subsequent infection. Enterococcal isolates were identified by colony morphology. The bacterial species was assessed and antibiotic susceptibilities were determined. A molecular analysis of 20 investigated enterococcal isolates revealed prevalence of commensal strain types; hospital-associated strain types or multi-resistant variants were absent. Cross transmission of E. faecium and E. faecalis isolates among neonatal patients attending the intensive crare unit at the same time was demonstrable. Introduction of hospital-associated, multi-resistant variants into this special setting has to be avoided to reduce the risk of subsequent infections.

Pressurized wet digestion in open vessels

The High Pressure Asher (HPA-S) was adapted with a Teflon liner for pressurized wet digestion in open vessels. The autoclave was partly filled with water containing 5% (vol/vol) hydrogen peroxide. The digestion vessels dipped partly into the water or were arranged on top of the water by means of a special rack made of titanium or PTFE-coated stainless steel. The HPA-S was closed and pressurized with nitrogen up to 100 bars. The maximum digestion temperature was 250 degrees C for PFA vessels and 270 degrees C for quartz vessels. Digestion vessels made of quartz or PFA-Teflon with volumes between 1.5 mL (auto sampler cups) and 50 mL were tested. The maximum sample amount for quartz vessels was 0.5-1.5 g and for PFA vessels 0.2-0.5 g, depending on the material. Higher sample intake may lead to fast reactions with losses of digestion solution. The samples were digested with 5 mL HNO(3) or with 2 mL HNO(3)+6 mL H(2)O+2 mL H(2)O(2). The total digestion time was 90-120 min and 30 min for cooling down to room temperature. Auto sampler cups made of PFA were used as digestion vessels for GFAAS. Sample material (50 mg) was digested with 0.2 mL HNO(3)+0.5 mL H(2)O+0.2 mL H(2)O(2). The analytical data of nine certified reference materials are also within the confidential intervals for volatile elements like mercury, selenium and arsenic. No cross contamination between the digestion vessels could be observed. Due to the high gas pressure, the diffusion rate of volatile species is low and losses of elements by volatilisation could be observed only with diluted nitric acid and vessels with large cross section. In addition, cocoa, walnuts, nicotinic acid, pumpkin seeds, lubrication oil, straw, polyethylene and coal were digested and the TOC values measured. The residual carbon content came to 0.2-10% depending on the sample matrix and amount.

Levels and risk assessment for humans and ecosystems of platinum-group elements in the airborne particles and road dust of some European cities

Traffic is the main source of platinum-group element (PGE) contamination in populated urban areas. There is increasing concern about the hazardous effects of these new pollutants for people and for other living organisms in these areas. Airborne and road dusts, as well as tree bark and grass samples were collected at locations in the European cities of Göteborg (Sweden), Madrid (Spain), Rome (Italy), Munich (Germany), Sheffield and London (UK). Today, in spite of the large number of parameters that can influence the airborne PGE content, the results obtained so far indicate significantly higher PGE levels at traffic sites compared with the rural or non-polluted zones that have been investigated (background levels). The average Pt content in airborne particles found in downtown Madrid, Göteborg and Rome is in the range 7.3-13.1 pg m(-3). The ring roads of these cities have values in the range 4.1-17.7 pg m(-3). In Munich, a lower Pt content was found in airborne particles (4.1 pg m(-3)). The same tendency has been noted for downtown Rh, with contents in the range 2.2-2.8 pg m(-3), and in the range 0.8-3.0 and 0.3 pg m(-3) for motorway margins in Munich. The combined results obtained using a wide-range airborne classifier (WRAC) collector and a PM-10 or virtual impactor show that Pt is associated with particles for a wide range of diameters. The smaller the particle size, the lower the Pt concentration. However, in particles <PM-10, some of the highest values correspond to the fraction <0.39 microm. Considering an average Pt content in all particles of approximately 15 pg m(-3), which is representative for all countries and environmental conditions, the tracheobronchial fraction represents approximately 10% and the alveolar fraction approximately 8% of the total particles suspended in air. However, from the environmental risk point of view, an exposure to PGEs in traffic-related ambient air is at least three orders of magnitude below the levels for which adverse health effects might theoretically occur (of approx. 100 ng m(-3)). Therefore, today inhalation exposure to PGEs from automotive catalysts does not seem to pose a direct health risk to the general population. Even though the data available today indicate no obvious health effects, there are still a number of aspects related to PGEs and catalysts that justify further research. First, continual monitoring of changes in PGE levels in air and road dust is warranted, to make sure that there is no dramatic increase from today's levels. Secondly, more detailed information on the chemical composition of the PGE-containing substances or complexes leaving the catalyst surface and the size distribution of the PGE-containing particles released during driving will facilitate a more in-depth human risk assessment.

Environmental risk of particulate and soluble platinum group elements released from gasoline and diesel engine catalytic converters

A comparison of platinum-group element (PGE) emission between gasoline and diesel engine catalytic converters is reported within this work. Whole raw exhaust fumes from four catalysts of three different types were examined during their useful lifetime, from fresh to 80,000 km. Two were gasoline engine catalysts (Pt-Pd-Rh and Pd-Rh), while the other two were diesel engine catalysts (Pt). Samples were collected following the 91441 EUDC driving cycle for light-duty vehicle testing, and the sample collection device used allowed differentiation between the particulate and soluble fractions, the latter being the most relevant from an environmental point of view. Analyses were performed by inductively coupled plasma-mass spectrometry (ICP-MS) (quadrupole and high resolution), and special attention was paid to the control of spectral interference, especially in the case of Pd and Rh. The results obtained show that, for fresh catalysts, the release of particulate PGE through car exhaust fumes does not follow any particular trend, with a wide range (one-two orders of magnitude) for the content of noble metals emitted. The samples collected from 30,000-80,000 km present a more homogeneous PGE release for all catalysts studied. A decrease of approximately one order of magnitude is observed with respect to the release from fresh catalysts, except in the case of the diesel engine catalyst, for which PGE emission continued to be higher than in the case of gasoline engines. The fraction of soluble PGE was found to represent less than 10% of the total amount released from fresh catalysts. For aged catalysts, the figures are significantly higher, especially for Pd and Rh. Particulate PGE can be considered as virtually biologically inert, while soluble PGE forms can represent an environmental risk due to their bioavailability, which leads them to accumulate in the environment.

Collaborative evaluation of the analytical state-of-the-art of platinum, palladium and rhodium determinations in road dust

In order to control the quality of platinum, palladium and rhodium determinations in road dust, the Standards, Measurements and Testing Programme (formerly BCR) of the European Commission has started a project, the final aim of which is to certify a road dust reference material for its contents of platinum group elements. The first part of this project consisted of an interlaboratory study, which aimed to test the feasibility of the preparation of a candidate road dust reference material and to detect and remove most of the pitfalls observed in platinum, palladium and rhodium determinations. This paper presents the main results of this interlaboratory study carried out prior to the certification campaign. The concordance of the data obtained by the participating laboratories for the three elements was considered to reflect the state-of-the-art and was encouraging enough to decide on the organization of a certification campaign to be conducted during the year 2000. The progress made with respect to the analytical state-of-the-art for these elements will be of great benefit to the quality of measurements carried out in environmental monitoring in this particular field.

Platinum-group elements: quantification in collected exhaust fumes and studies of catalyst surfaces

Automotive catalytic converters, in which Pt, Pd and Rh (platinum-group elements; PGEs) are the active components for eliminating several noxious components from exhaust fumes, have become the main source of environmental urban pollution by PGEs. This work reports on the catalyst morphology through changes in catalyst surface by scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDX) and laser-induced breakdown spectrometry (LIBS) from fresh to aged catalytic converters. The distribution of these elements in the fresh catalysts analysed (Pt-Pd-Rh gasoline catalyst) is not uniform and occurs mainly in a longitudinal direction. This heterogeneity seems to be greater for Pt and Pd. PGEs released by the catalysts, fresh and aged 30,000 km, were studied in parallel. Whole raw exhaust fumes from four catalysts of three different types were also examined. Two of these were gasoline catalysts (Pt-Pd Rh and Pd-Rh) and the other two were diesel catalysts (Pt). Samples were collected following the 91,441 EUDC driving cycle for light-duty vehicle testing. The results show that at 0 km the samples collected first have the highest content of particulate PGEs and although the general tendency is for the release to decrease with increasing number of samples taken, exceptions are frequent. At 30,000 km the released PGEs in gasoline and diesel catalysts decreased significantly. For fresh gasoline catalysts the mean of the total amount released was approximately 100, 250 and 50 ng km(-1) for Pt, Pd and Rh, respectively. In diesel catalysts the Pt release varied in the range 400-800 ng km-1. After ageing the catalysts up to 30,000 km, the gasoline catalysts released amounts of Pt between 6 and 8 ng km(-1), Pd between 12 and 16 ng km(-1) and Rh between 3 and 12 ng km(-1). In diesel catalysts the Pt release varied in the range 108-150 ng km(-1). The soluble portion of PGEs in the HNO3 collector solution represented less than 5% of the total amount for fresh catalysts. For 30,000 km the total amount of soluble PGEs released was similar or slightly higher than for 0 km.