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The used pressures during growth with PLD vary from base pressure (often in the 10β7 mbar range) to 10β4 mbar O2. Crystallization of YSZ on the silicon crystal lattice is typically observed after deposition of about 1 nm6,9. In the second step, after deposition of about 5 nm, more oxygen is added to fully oxidize the film during the remainder of the growth. Control of the chemistry during the first step seems to be critical for the crystalline quality of the resulting film. Deposition of too large amounts of YSZ in reducing conditions leads to formation of silicides, which increases the amount of defects in the YSZ film20. Furthermore, the presence of residual native oxide may aid the crystallization of YSZ by avoiding the large lattice mismatch between Si and YSZ (5.7%), either via lateral overgrowth20 or via crystallization on the crystalline part of the native oxide, which may be situated close to the silicon surface with lattice parameters closer to YSZ18,21.
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The work described above shows the occurance and importance of several chemical processes during initial growth of YSZ on Si by PLD, e.g. silicon oxide reduction and silicide formation. However, limited attention has been paid to the possibilities to control these different chemical processes. An unique feature of the PLD process is the interaction of the plasma with the background gasses present in the deposition chamber. The metals in the plasma can obtain different degrees of oxidation depending on the partial oxygen pressure22. As shown for the homoepitaxial growth of SrTiO3 (STO), stoichiometry and growth kinetics depend heavily on the degree of oxidation of the plasma. Furthermore, the STO substrate proved to supply oxygen to the growing STO film as well23. Similar to the growth of STO on STO, three sources of oxygen can be distinghuised during growth of YSZ on Si with native oxide. At the substrate/film surface, oxygen can arrive from the plasma as atomic or molecular oxygen, or in the form of (partially) oxidized zirconium and yttrium. The oxygen from the background can oxidize the growing film directly, but also interact with the plasma. Furthermore, oxygen is present in the silicon native oxide. The thickness of this oxide can change during heating to the YSZ growth temperature due to reaction with oxygen from the background. Since oxygen is involved in all of the chemical processes described before, tuning the contributions of all sources of oxygen may provide a way to control the chemistry during the scavenging process.
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In this work, the possibility to control the chemistry of the initial growth of YSZ on Si was investigated, as well as the relationship between the chemistry and the resulting crystalline properties of the YSZ film. Both subjects were assessed by detailed study of the PLD growth process, with a focus on the contributions of the different sources of oxygen. In order to investigate these contributions, all sources were adressed individually:Background pressure. The contribution of oxygen from the background was varied by changing the partial oxygen pressure (pO2) at constant total pressures. Ar was used to reach the total pressure aimed for, since it is inert and has an atomic weight close to the weight of molecular oxygen. In this way, the plasma plume size and shape was kept similar, meaning the flux of oxygen from the background could be changed independently from the Zr and Y fluxes from the plasma. Additionally, the fluxes of Zr and Y from the plasma could be changed independently by changing the laser repetition rate.Plasma. The physics and chemistry of the plasma changes drastically with pressure22,24. For instance, the oxidation state of the plasma upon arriving at the substrate can be different for similar pO2, while the total pressure influences the arrival time and plasma temperature. For this reason, 2 different total pressures were examined, i.e. 2*10β2 and 1*10β1 mbar. The resulting physics and chemistry of the plasma were examined with self-emission spectroscopy.Native oxide. All 5 Γ 5 mm Si substrates were cut from the same 4 inch wafer in order to start with the same native oxide thicknesses in all experiments. However, the thickness can change due to heating of the substrate in the presence of oxygen. Therefore, in situ X-ray Photoelectron Spectroscopy (XPS) was used to determine silicon oxide thicknesses of the substrates in different deposition conditions.
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Background pressure. The contribution of oxygen from the background was varied by changing the partial oxygen pressure (pO2) at constant total pressures. Ar was used to reach the total pressure aimed for, since it is inert and has an atomic weight close to the weight of molecular oxygen. In this way, the plasma plume size and shape was kept similar, meaning the flux of oxygen from the background could be changed independently from the Zr and Y fluxes from the plasma. Additionally, the fluxes of Zr and Y from the plasma could be changed independently by changing the laser repetition rate.
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Plasma. The physics and chemistry of the plasma changes drastically with pressure22,24. For instance, the oxidation state of the plasma upon arriving at the substrate can be different for similar pO2, while the total pressure influences the arrival time and plasma temperature. For this reason, 2 different total pressures were examined, i.e. 2*10β2 and 1*10β1 mbar. The resulting physics and chemistry of the plasma were examined with self-emission spectroscopy.
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Native oxide. All 5 Γ 5 mm Si substrates were cut from the same 4 inch wafer in order to start with the same native oxide thicknesses in all experiments. However, the thickness can change due to heating of the substrate in the presence of oxygen. Therefore, in situ X-ray Photoelectron Spectroscopy (XPS) was used to determine silicon oxide thicknesses of the substrates in different deposition conditions.
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The results section is divided into two parts. First, chemical and crystallization processes observed during initial growth in the different conditions are described, as well as the resulting crystalline properties. Reflection High-Energy Electron Diffraction (RHEED) was used to monitor the crystallization process during growth. In order to investigate the chemistry after growth, in situ X-ray Photoelectron Spectroscopy (XPS) was used. X-ray Diffraction (XRD) and Atomic Force Microscopy (AFM) were used to relate the observed growth processes to respectively the crystalline properties and morphology of the films. Secondly, the contributions of the different sources of oxygen to those chemical and crystallization processes were investigated, as described above.
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First, the influence of pO2 on the chemical interactions during initial growth was investigated. Figure 1a shows XPS spectra of 6 nm YSZ films grown at different pO2, while the total pressure and laser repetition rate were kept constant at respectively 2*10β2 mbar Ar and 14 Hz. Zr silicide formation was clearly observed when a pO2 of 1*10β6 mbar was used, as concluded from the existence of Zr0 peaks together with a shoulder at the low binding energy side of the Si2p bulk peak25. The intensities of these features were lower at 1*10β5 mbar, and were completely absent when pO2 of 1*10β4 mbar or higher were used. A similar change was obtained by changing the flux of Zr and Y using different laser repetition rates. The XPS spectra in Fig. 1b show that silicide formation decreased when the laser repetition rate was decreased from 28 to 14 Hz at a constant pO2 of 1*10β5 mbar, whereas no silicide formation was detected anymore at 7 Hz. Thus, the formation of Zr silicides can be controlled by tuning the ratio between flux of oxygen from the background gas and Zr and Y from the plasma. Although similar trends can be expected for Y, the changes in binding energies are too small to clearly identify the different phases (see Supplementary Fig. S1).Figure 1(a) XPS Zr3d and Si2p spectra of films grown at total pressures of 2*10β2 mbar at (a) different pO2 or (b) with different laser repetition rates. A low flux of oxygen compared to Zr, caused by low pO2 or high laser repetition rate, led to silicide formation and an increased ratio of silicate/SiOx to SiO2 bonds.
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(a) XPS Zr3d and Si2p spectra of films grown at total pressures of 2*10β2 mbar at (a) different pO2 or (b) with different laser repetition rates. A low flux of oxygen compared to Zr, caused by low pO2 or high laser repetition rate, led to silicide formation and an increased ratio of silicate/SiOx to SiO2 bonds.
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A second notable difference appeared in the Si2p region indicating oxidized species. In the Si2p region, peaks around 99.7 eV and103.5 eV indicate the Si0 substrate and completely oxidized Si4+ respectively. In between both extremes, underoxidized Si (SiOx) and/or silicates (Y/Zr-O-Si) can appear26. In principle, at least one monolayer of silicate bonds is expected due to the interface between YSZ and Si or SiO2, which contributes significantly to the XPS spectra due to the surface sensitivity of XPS. As visible in Fig. 1, the region indicating SiO2 increased with respect to the region indicating silicates and SiOx species when the pO2 was increased or the laser repetition rate was decreased. Although any quantification cannot be performed without knowledge about the morphology and distribution of the different species, the measurements suggest increasing regrowth of SiO2 with increasing pO2 or decreasing laser repetition rate. Quantification of the SiO2 thickness will be discussed later.
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In order to investigate the influence of the initial chemistry on the crystalline properties of YSZ, 100 nm YSZ films were grown on top of 5 nm films which were grown under varying pO2 and a fixed laser repetition rate of 14 Hz. This laser repetition rate was chosen because of the clear oxygen pressure dependent differences in chemistry during initial growth, as shown by the XPS measurements above. The 100 nm films were all grown with the same depostion conditions (p = 2 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\ast $$\end{document}β 10β2 mbar O2, f = 14 Hz). In this way, XRD measurements of the thick films acted as a tool to indicate the crystalline properties of the first 5 nm. The XRD measurements presented in Fig. 2 show a clear trend in crystalline properties depending on the pO2 at 2*10β2 mbar Ar during initial growth. At low pO2, (111) oriented YSZ was measured besides the epitaxial (001) orientation (besides the RHEED patterns shown in Fig. 2, see Supplementary Fig. S2 for a Ο-scan confirming the epitaxial relation between Si and YSZ). The intensity of the (111) peak decreased with increasing pO2. At the same time, the FWHM of the rocking curve of the (002) peak decreased. At a pO2 of 5*10β3 mbar, the lowest FWHM was measured, while no (111) orientation was visible anymore. Increasing the pO2 above this value led to increased values of the FWHM and the presence of (111) oriented YSZ again.Figure 2XRD measurements of 100 nm thick YSZ films on top of 5 nm YSZ films grown in varying pressures. (a) XRD ΞΈ β 2ΞΈ scans of the films with the first 5 nm grown at a total pressure of 2*10β2 mbar Ar. At 33Β° a multiple reflection peak of the Si can be observed. The variation in intensity of this peak is only related to the in-plane orientation of the sample in the XRD40. (b) FWHM of the YSZ (002) rocking curves of the samples with the initial 5 nm grown in total pressures of 2*10β2 or 1*10β1 mbar. The dashed lines are inserted for visual reference. (cβf) RHEED images corresponding to the films shown in subfigure a, after growth of 5 nm in respectively 1*10β5, 1*10β4, 5*10β3 and 2*0β2 mbar. The images were taken after adding the 0.02 mbar O2 to the growth chamber for growth of the 100 nm layer. (gβi) RHEED images of the same samples after growth of the 100 nm layer in 0.02 mbar O2. The rings indicated by a green arrow are artefacts formed by reflection of the electron beam at its entrance pinhole to the growth chamber.
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XRD measurements of 100 nm thick YSZ films on top of 5 nm YSZ films grown in varying pressures. (a) XRD ΞΈ β 2ΞΈ scans of the films with the first 5 nm grown at a total pressure of 2*10β2 mbar Ar. At 33Β° a multiple reflection peak of the Si can be observed. The variation in intensity of this peak is only related to the in-plane orientation of the sample in the XRD40. (b) FWHM of the YSZ (002) rocking curves of the samples with the initial 5 nm grown in total pressures of 2*10β2 or 1*10β1 mbar. The dashed lines are inserted for visual reference. (cβf) RHEED images corresponding to the films shown in subfigure a, after growth of 5 nm in respectively 1*10β5, 1*10β4, 5*10β3 and 2*0β2 mbar. The images were taken after adding the 0.02 mbar O2 to the growth chamber for growth of the 100 nm layer. (gβi) RHEED images of the same samples after growth of the 100 nm layer in 0.02 mbar O2. The rings indicated by a green arrow are artefacts formed by reflection of the electron beam at its entrance pinhole to the growth chamber.
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The corresponding RHEED patterns revealed similar information. Rings were observed after growth of 5 nm in 1*10β5 mbar O2, indicating the presence of polycrystalline phases (see Fig. 2c). The presence of polycrystalline phases was consistent with the presence of the (111) orientation measured with XRD. Other orientations were hardly visible in the XRD spectra due to the low relative intensities of these peaks. Typically, streaks, indicating a flat surface, appeared when the FWHM of the XRD (002) rocking curve was below 1Β° (see Fig. 2e), while spots, indicating a rougher surface, appeared above this value (Fig. 2d,f). In all cases, the sharpness of the RHEED spots or streaks increased after growth of the 100 film YSZ film (see Fig. 2gβj), indicating improved surface crystallinity. Even in the case rings were observed after growth of the 5 nm film, a well-defined pattern evolved gradually during growth of the 100 nm film (see Fig. 2g).
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A similar trend was observed when the initial growth was performed at a total pressure of 1*10β1 mbar (see Fig. 2b). The growth rate per second was kept similar to the 2*10β2 mbar experiments by using a laser repetition rate of 12.5 Hz. Despite the equal growth rate, the lowest FWHM was observed at 5*10β4 mbar, which is one order of magnitude lower compared to the growth performed at a total pressure of 2*10β2 mbar. The lowest FWHM was 1.00Β°, while an optimum of 0.85Β° was obtained in the 2*10β2 mbar case. Furthermore, features indicating polycrystallinity started to dominate the RHEED pattern at 5*10β3 mbar, while streaks or spots indicating epitaxial phases were not observed at all at a pO2 of 2*10β2 mbar. This degree of polycrystallinity differed from the growth performed at a total pressure of 2*10β2 mbar, since only a small amount of polycrystalline phases was observed with XRD when 2*10β2 mbar O2 was used (see Fig. 2a).
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During growth of the films, RHEED movies were recorded with ~0.1 frame/s in order to obtain insights about the crystallization behavior in the different growth conditions. Figure 3a presents an example of the analysis performed on the RHEED data. Before start of the growth, the pattern of the crystalline surface buried beneath the amorphous silicon oxide was visible. This pattern faded when YSZ was deposited due to increased attenuation by the deposited material. After a certain deposition time, streaks or spots indicating epitaxial YSZ appeared. The intensity of a disappearing Si spot and evolving YSZ streak or spot was monitored over time. The minimum intensity was used as an indication of the crystallization time. This crystallization time serves as an indication of the efficiency of the native oxide decomposition and the following YSZ crystallization, and therefore reveals important details about the YSZ growth mechanism, as will be described in more detail in the discussion section. Figure 3b shows the crystallization times as well as the corresponding amount of deposited YSZ, determined for samples grown at different pO2 and total pressures of 2*10β2 or 1*10β1 mbar Ar. Similar trends were visible in the crystallization time for both total pressures. First the crystallization time decreased with increasing pO2, after which it increased again. At a total pressure of 1*10β1 mbar, the minimum in crystallization time was observed at the same pO2 as the optimum crystalline quality (see Fig. 2). At the total pressure of 2*10β2 mbar, a minumum was observed at a pO2 of 1*10β5 mbar, after which the crystallization time slightly increased. Crystallization times were notably larger at 1*10β1 mbar.Figure 3(a) Snapshots from a RHEED movie recorded during growth at 5*10β3 mbar O2 in a total pressure of 2*10β2 mbar Ar. Below the snapshots, the intensity profile derived from the blue box and the streak positions derived from the green box are presented. The dashed line indicates the minimum intensity, which is taken as a measure of the crystallization time/thickness. (b) Crystallization times/thicknesses derived with the method depicted in subfigure (a), for samples grown at different pO2 in total presures of 2*10β2 and 1*10β1 mbar Ar. The dashed lines are a guide to the eye.
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(a) Snapshots from a RHEED movie recorded during growth at 5*10β3 mbar O2 in a total pressure of 2*10β2 mbar Ar. Below the snapshots, the intensity profile derived from the blue box and the streak positions derived from the green box are presented. The dashed line indicates the minimum intensity, which is taken as a measure of the crystallization time/thickness. (b) Crystallization times/thicknesses derived with the method depicted in subfigure (a), for samples grown at different pO2 in total presures of 2*10β2 and 1*10β1 mbar Ar. The dashed lines are a guide to the eye.
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Figure 3a shows a typical example of the change of the positions of the Si and YSZ streaks with increasing deposition time. No change in the distance between the YSZ streaks was observed above 2 nm, even after growth of additional 100 nm in oxygen atmosphere. The distance between the YSZ streaks was larger compared to Si, indicating a smaller lattice, as expected. Below 2 nm, the YSZ streak positions were closer to the Si streak positions. Although this may indicate that YSZ was initially strained to the silicon, the shift can be caused by overlap with the Si streaks, which were still weakly present at the starting point of YSZ crystallization. Similar fast lattice relaxation during growth was observed for all films.
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Figure 4a shows the Si2p spectra for silicon substrates with native oxide after annealing at 800 Β°C for 5 minutes at different pO2. An increase in the intensity of SiO2 with respect to Si from the bulk of the substrate was notable above a pO2 of 1*10β4 mbar. Using the model described in the methods section, the silicon oxide thicknesses were calculated from these spectra. A linear increase of oxide thickness with pO2 was observed, as shown in Fig. 4b. Growth of YSZ was normally started within 30 seconds after reaching 800 Β°C. This is especially important for the higher pO2, since the thickness of the silicon oxide is expected to increase approximately linearly with time27. For example, when growth is performed at a total pressures of 2*10β2 mbar O2, the increase in oxide thicknes is expected to be only 0.04 nm when the substrate is kept at 800 Β°C for 30 s, instead of the observed 0.4 nm when the substrate is kept at 800 Β°C for 5 min. Indeed, polycrystalline growth was observed in the latter case (data not shown), while epitaxial growth was observed when the growth started immediately after reaching 800 Β°C (see Fig. 2).Figure 4(a) XPS Si2p spectra of Si substrates after heating to 800 Β°C at different pO2. Increase of oxide thickness was observed above 1*10β4 mbar. (b) Calculated silicon oxide thicknesses for as received and annealed substrates, and after growth of YSZ. The silicon oxide thicknesses for the samples with YSZ film were calculated from the samples shown in Fig. 1a, i.e. 6 nm YSZ films grown at a total pressure of 2*10β2 mbar with a laser repetition rate of 14 Hz. The black line is a linear fit of the data..
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(a) XPS Si2p spectra of Si substrates after heating to 800 Β°C at different pO2. Increase of oxide thickness was observed above 1*10β4 mbar. (b) Calculated silicon oxide thicknesses for as received and annealed substrates, and after growth of YSZ. The silicon oxide thicknesses for the samples with YSZ film were calculated from the samples shown in Fig. 1a, i.e. 6 nm YSZ films grown at a total pressure of 2*10β2 mbar with a laser repetition rate of 14 Hz. The black line is a linear fit of the data..
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Secondly, the SiO2 thicknesses after growth of YSZ were calculated for the samples grown in a total pressure of 2*10β2 mbar. In order to perform the calculation, a homogeneous Si-SiO2-YSZ stacking sequence was assumed. After fitting, only the parts of the spectra indicating SiO2 and Si were taken into account by subtracting the silicide, silicate and SiOx contributions, which were especially present in the low pO2 samples. A significant increase in silicon oxide thickness with increasing pO2 was calculated, as shown in Fig. 4b. Although the samples were cooled down in vacuum directly after growth, the oxide thicknesses were much larger compared to the bare substrates annealed at the same pO2. In the case of growth at pO2 = 5*10β3 mbar, where an optimum crystalline quality was observed with XRD, a silicon oxide thickness of 2.6 nm was determined.
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The chemistry and kinetics of the plasma were investigated for different pO2 at total pressures of 2*10β2 and 1*10β1 mbar. Figure 5 presents the front position versus delay time of the plasma plume at pressures of 2*10β2 and 1*10β1 mbar O2. The plasmas propagated differently in both pressures. At 2*10β2 mbar, the plasma arrived at the substrate 6 ΞΌs after ablation, with a velocity of 5 km/s. The propagation could be fitted with a simple kinetic drag model28. In this model, the plasma has a ballistic like propagation, while minor deceleration occurs due to drag forces on the particles in the plasma. At 1*10β1 mbar, the plasma front position changed linearly with delay time after 12 ΞΌs, which indicates propagation by diffusion. The plasma reached the substrate after 20 ΞΌs with a velocity of 1 km/s. The plasma propagation behavior and arriving velocities were very similar to other oxide plasmas24.Figure 5Plot of plasma front positions versus delay times at 2*10β2 and 1*10β1 mbar O2. The solid lines represent a drag model fit, the dashed curve is a linear fit indicating diffusive propagation. The blue line is the substrate position.
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Figure 6a,c shows the spectra of the plasmas at different pO2 just after arriving at the substrate. The spectra show a clear trend depending on pO2 for both 2*10β2 and 1*10β1 mbar total pressures. Comparison with spectra from the binary oxides and reference tables29,30 showed that the plasmas were dominated by atomic Zr lines at low pO2. Especially, the lines between 400 and 500 nm can be assigned to atomic Zr species. The relative intensity in this region decreased with increasing pO2. Simultaneously, between 500 and 600 nm bands originating from zirconia increased. With increasing oxidation, the contribution of yttria to the spectra became stronger as well. Especially, a strong YO band showed up at 597 nm. In order to compare the oxidation of the plasmas, the relative intensity of this line was determined for all pO2 after different delay times. Figure 6b,d show the results for the total pressures of 2*10β2 and 1*10β1 mbar respectively. The presence of the YO line was noted above pO2 of 1*10β4 mbar in 2*10β2 mbar total pressure, and 5*10β4 mbar in the 1*10β1 mbar case. When the plasma arrived at the substrate, the YO line was more pronounced at total pressures of 1*10β1 mbar, compared to similar pO2 in 2*10β2 mbar. However, at 2*10β2 mbar, the relative intensity of the YO still increased after arrival, while the increase hardly occurred at 1*10β1 mbar. For both total pressures, oxidation was observed at pO2 corresponding to optimal YSZ quality (5*10β3 and 5*10β4 for 0.02 and 1*10β1 mbar respectively, see Fig. 2).Figure 6Self emission spectra of the plasma at total pressures of (a) 2*10β2 and (c) 1*10β1 mbar after arriving at the substrate, respectively 6 and 20 ΞΌs after ablation. The YO line at 597 nm is indicated with a black arrow. (b,d) Show the relative intensities of the YO line at 597 nm after different delay times for total pressures of 2*10β2 and 1*10β1 mbar respectively. The color scales correspond to subfigures (a,c), the arrivial of the plasma plume at the substrate is indicated with a dashed line.
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Self emission spectra of the plasma at total pressures of (a) 2*10β2 and (c) 1*10β1 mbar after arriving at the substrate, respectively 6 and 20 ΞΌs after ablation. The YO line at 597 nm is indicated with a black arrow. (b,d) Show the relative intensities of the YO line at 597 nm after different delay times for total pressures of 2*10β2 and 1*10β1 mbar respectively. The color scales correspond to subfigures (a,c), the arrivial of the plasma plume at the substrate is indicated with a dashed line.
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A high ratio of Y/Zr to oxygen during growth caused formation of silicides, which could be tuned by changing the pO2 and the laser repetition rate. As shown for the case of a laser repetition rate of 14 Hz and a total pressure of 2*10β2 mbar, silicide formation occurred at pO2 below 1*10β5 mbar. At these conditions, plasma spectroscopy did not show any oxidation of the plasma. Initially, Y and Zr can take sufficient oxygen from the native oxide to form YSZ. However, oxygen deficiency may occur due to ongoing deposition of metal atoms. Oxygen deficiency makes YSZ unstable towards silicide formation when contacted with silicon31. In a pO2 of 1*10β5 mbar, the thermodynamically expected amount of vacancies is much lower than the amount causing instability31, while the flux of oxygen from the ambient should be sufficient to provide the necessary oxygen for complete oxidation of the growing film, considering the used growth speed (~0.5 unit cells per second at 14 Hz). Apparently, excess of O2 at the film surface is necessary to completely oxidize the film during growth.
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Silicide formation explains the trend in the crystallization time at low pO2. In principle, the scavenging process, followed by YSZ crystallization, should be fastest in the most oxygen deficient conditions, i.e. when Y and Zr do not oxidize in the plasma and regrowth of the silicon oxide due to oxygen from the background gas is limited. Instead, increased crystallization times were observed in the most oxygen deficient conditions, which can be caused by competition between silicide formation and YSZ crystallization at the silicon-YSZ interface. In the higher pO2 regime, the crystallization time increased with increasing pO2. For both the total pressures of 2*10β2 and 1*10β1 mbar, the increase occurred in the regime where the plasma started to oxidize. Due to this partial oxididation, the scavenging possibility per Zr or Y atom was lower, meaning more YSZ was needed to break down the silicon native oxide.
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Two additional mechanisms were found to contribute to the increased crystallization times. First of all, at pressures above 1*10β3, the silicon oxide thickness started to increase before start of the growth. This contribution was largely circumvented by starting the growth quickly after reaching the growth temperature. More importantly, the thickness of the silicon oxide after growth of YSZ depended heavily on the pO2, and showed a growth rate much higher than the growth rate on the as received silicon. Similar growth rate enhancement with over an order of magnitude has been described for thin metal overlayers of e.g. Ba32, Cu33, Sr34 and Y35. Apparently, YSZ catalyzes the absorption of oxygen by the silicon oxide. Therefore, silicon oxide regrowth is expected to compete with the scavenging process as soon a YSZ is present at the silicon surface. In the case of growth in a total pressure of 2*10β2 mbar, the optimum pO2 was found at conditions were severe regrowth of the silicon oxide was observed. Together with the observed partial oxidation of the plasma, the scavenging process in optimum conditions can now be summarized by the following reaction:2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$Zr{O}_{2-x}+xSi{O}_{2}+{O}_{2}+Si\to xSiO\uparrow +Zr{O}_{2}+Si{O}_{2}$$\end{document}ZrO2βx+xSiO2+O2+SiβxSiOβ+ZrO2+SiO2
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If the oxygen pressure is too high, (partly) polycrystalline films grow due to insufficient scavenging power, mainly caused by overoxidation of the plasma and regrowth of the native oxide. Note that the crystallization times correlated well with the crystalline quality of the grown films. In general, low crystallization times led to low FWHM of the YSZ (002) rocking curves (compare Figs 2b and 3b), since both silicide formation and overoxidation of the plasma were avoided.
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The observed phenoma agree very well to the lateral overgrowth mechanism proposed by De Coux et al.20, since regrowth of silicon oxide does not necesseraly prevent lateral crystallization. The observed lattice relaxation from the start of crystallization fits this mechanism as well, and is in agreement with the observations made by Ishigaki et al.18. Lateral overgrowth is a well known method in growth of semiconductors, and proved to increase the crystalline quality due to avoidance of defect formation because of strain36,37. Similarly, the high YSZ crystalline qualities in conditions were residual SiO2 is expected, can be explained by this mechanism. As shown in Supplementary Fig. S3, a low surface roughness was obtained as well, as expected for high crystalline quality films. On the other hand, surfaces in silicide forming conditions were much rougher, due to a more local YSZ nucleation and lower crystalline qualities, as shown in more detail in the Supplementary Information (see Supplementary Figs S3βS5).
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The trends described above hold in general for both total pressures of 2*10β2 mbar and 1*10β1 mbar. However, differences where observed in the optimal pO2, crystallization times, the obtained crystalline quality and the limiting pO2 at which epitaxial growth was not possible anymore. Some aspects of the growth process were similar for both total pressures. The silicon oxide thicknesses at the start of YSZ growth were similar, since the increase in thickness depends on the pO2 only. For the same reason, the fluxes of oxygen from the ambient to the growing film were similar. Finally, the flux of YSZ per second was kept constant by using a slightly lower laser repetition rate in the 1*10β1 mbar case (12.5 Hz in stead of 14 Hz). Therefore, the differences in growth behavior can only be explained by differences in the behavior of the plasma.
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First, differences can be caused by the different kinetic regimes of the plasma. At 2*10β2 mbar, the velocity of the plasma arriving at the substrate was much higher compared to 1*10β1 mbar. High energetic particles may assist in breaking of silicon-oxygen bonds within the native oxide layer. Secondly, differences can be caused by the plasma chemistry. A higher degree of oxidation is expected at 1*10β1 mbar, since the plasma is thermalized23. Furthermore, the interaction between the plasma and background gas is expected to be increased at 1*10β1 mbar, because of the diffusion like propagation. Surprisingly, the pO2 at which plasma oxidation started was in the same order of magnitude for both total pressures. This observation is however in agreement with the observations made on plasmas ablated from an YBiO3 target38. In that case, oxidation of Y was observed quickly after ablation because of reaction with oxygen ablated from the target. At lower pO2, the pressure dependent degree of oxidation was explained by a pressure dependent oxygen nonstoichiometry of the target. If this mechanism is true, the degree of oxidation is indeed expected to be comparable in both total pressures. At low pO2, the interaction of the plasma with oxygen from the background is low in both total pressures. Therefore, the oxidation of the plasma is dominated by the oxygen present in the target, which depends only on the pO2. The plasma chemistry can however still be responsible for observed differences in growth behavior due to different arrival times. In the 2*10β2 mbar case, the plasma just started to oxidize when arriving at the substrate, while the amount of oxidation was higher in the 1*10β1 mbar case due to the increased arrival time. Therefore, the average amount of oxidized species arriving at the substrate was lower at 2*10β2 mbar compared to 1*10β1 mbar.
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More work should be performed in order to elucidate the details of the influence of the plasma kinetics and chemistry on the growth process. This is important, since a proper choice of the total pressure can be used to tune the oxygen arriving from the plasma with respect to the oxygen arriving from the ambient. Furthermore, the velocity of the particles arriving at the substrate can be optimized in order to optimize the scavenging process.
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In this work, the growth mechanism of epitaxial YSZ on Si with native oxide by PLD was investigated. The possibility to control different sources of oxygen in the PLD process was exploited to control the chemistry during the scavenging of oxygen from the native oxide by YSZ. In conditions corresponding to optimum YSZ crystalline quality, silicide formation was prevented due to partial oxidation of the YSZ plasma and sufficient flux of oxygen from the ambient to the growing film. In this regime, significant regrowth of silicon oxide occurred, catalyzed by the deposited YSZ film. Thickness increase of the silicon oxide before growth had to be prevented by starting the depostion as soon as possible after reaching growth temperature. These findings show that the contributions of all sources of oxygen can and should be controlled in order to obtain reproducible YSZ growth.
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study
| 100.0 |
All films were grown in a TSST PLD chamber with in situ RHEED (STAIB). A 248 nm KrF laser (Coherent LPXpro) was used for ablation from a polycrystalline YSZ target. The base pressure of the PLD chamber was in the 10β8 mbar range. For low partial oxygen pressures, the oxygen flow was regulated with a needle valve, while the flow of Ar was regulated with a mass flow controller. The substrates were heated via laser heating. The deposition parameters are summarized in Table 1. Samples examined with in situ XPS were cooled down in vacuum, while the thicker samples examined with XRD were cooled down in 100 mbar O2.Table 1Parameters for YSZ deposition.Substrate temperature (Β°C)800Heating rate (Β°C)50Cooling rate (Β°C)20Fluency (J/cm2)1.9Spot size (mm2)2.4Laser repetition rate (Hz)VariedTotal background pressure (mbar)0.02 or 0.1Partial oxygen pressur (mbar)VariedTarget-substrate distance (mm)50The conditions which were varied are described in the results section.
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study
| 100.0 |
In situ XPS was performed with an Omicron XM-1000 monochromated Al-KΞ± source, with the pass energy to the detector set to 20 eV. The angle of the surface normal with respect to the detector was 1Β°. The method to determine silicon oxide thickness was similar to the 5P* method described by Seah and Spencer39. An R0 value of 0.80 was determined by measuring silicon substrates with different thicknesses of thermally grown oxides. An attenuation length of photoelectrons in silicon dioxide of 3.448 nm was used39.
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| 100.0 |
The chemistry of the YSZ plasma plume was assessed by self emission plasma spectroscopy. An Andor Shamrock 163 spectograph with a 300 lines/mm grating and an Andor iStar ICCD detector with 1024 Γ 1024 pixels were used to collect the data. This combination of spectrograph and detector resulted in a bandpass of 257 nm and a spectral resolution of 1.5 nm. The gate width was adjusted with the delay time after ablation, and typically kept below 2% of the delay time. The resulting images obtained with the CCD camera consisted of one axis representing the wavelenght, and the other axis representing the spatial component. In order to compare the measurements, the intensities were summed along the spatial axis. All spectra were normalized between 0 and 1 after subtracting the minimum intensity. The wavelength scale was calibrated using reference tables29,30. In order to obtain information about the individual oxides, sintered powder targets of ZrO2 and Y2O3 were examined as well. The time of arrival and velocity of the YSZ plasma plume at the substrate were measured by imaging the visible part of the plasma, i.e. without a spectrograph between the plasma and the camera.
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study
| 100.0 |
Brain metastases (BM) occur in 20-40% of patients with non-small cell lung cancer (NSCLC) at some point during the disease course . NSCLC is heterogeneous in terms of its histological subtypes and distinct driving oncogenes , which may affect the development of BM. Adenocarcinoma histology has been reported to be associated with BM from NSCLC. Epidermal growth factor receptor (EGFR) is one of the most common oncogenes, activating mutations of which drive tumor growth in NSCLC. The association between the EGFR mutation status and BM in patients with NSCLC has been noted in the past [3β6]. However, these findings have not been consistently observed. It is unclear whether the EGFR mutation status can predict the occurrence of subsequent BM (SBM) in advanced NSCLC or whether the high frequency of BM in EGFR-mutated NSCLC can be mainly attributed to the survival factor of EGFR mutations. Moreover, the rationales behind the above findings are not well determined. In addition, evidence suggests that EGFR exon 19 deletion-positive NSCLC is distinct from EGFR exon 21 (L858R) point mutation-positive NSCLC with regard to the tumor response to treatment and patient survival [7β10]. Nonetheless, the question regarding whether these two common subtypes of EGFR mutations have different impacts on the occurrence of BM in NSCLC has not been well addressed.
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review
| 99.8 |
EGFR tyrosine kinase inhibitors (TKI), such as gefitinib, erlotinib or afatinib, preferentially target lung tumors with mutated-EGFRs, but not the wild-type EGFR (WT-EGFR) tumors, suggesting that the mutated- and WT-EGFRs have different oncogenic effects. EGFR protein expression was previously detected in various solid tumors, and EGFR expression correlated with cell migration/invasion in breast and oral cancer cell lines [11β13]. However, the ability of EGFR to enhance cell motility is ligand-dependent [11β13]. The participation of activating EGFR mutations in lung cancer cell mobility is unknown.
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| 99.94 |
Therefore, in this study, we determined whether EGFR mutations, including the exon 19 deletion and L858R point mutation subtypes, predict the occurrence of the SBM in NSCLC patients, and characterized the role of activating EGFR mutations in lung cancer cell dissemination.
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study
| 100.0 |
Of 596 NSCLC patients, 384 had a determined EGFR mutation status and were eligible for further analysis (Figure 1). This group had a median age of 68.1 years (interquartile range: 58.0-78.0 years) and a median follow-up time of 11.8 months (interquartile range: 3.9-24.8 months); 79 (20.6%) survived to the last follow-up.
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study
| 100.0 |
Of the 596 non-small cell lung cancer (NSCLC) patients, 384 with a determined epidermal growth factor receptor (EGFR) mutation status, including 186 (48.4%, 186/384) with any or combined mutations of EGFR exon 18 to 21 and 198 with wild-type (WT) EGFR, were eligible for the identification of brain metastases (BM).
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study
| 99.94 |
Mutated-EGFRs were found in 186 (48.4%) of the 384 eligible patients (Figure 1), including an in-frame deletion in exon 19 (n = 79), a point mutation (L858R) in exon 21 (n = 97), and uncommon mutations (n = 10, 3 with an exon 18 point mutation, 6 with an exon 20 mutation, and 1 with an exon 18 and 20 mutation). The median OS of the mutated and WT patients was 20.6 months and 7.8 months, respectively (P < 0.001). The majority of the enrolled patients with stage IIIB-IV disease received cytotoxic chemotherapy and some received EGFR-TKIs (the first-generation) as the 1st-line care during the study period (Supplementary Materials and Methods). Of the 384 patients, 150 (39.1%) experienced BM, including 87 with BM at the diagnosis of their lung cancer and 63 with SBM during the follow-up period. Of 150 BM patients, 96 (64%) had mutated-EGFR and 54 had WT-EGFR.
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study
| 99.94 |
The patientsβ characteristics at the time of their NSCLC diagnosis are shown in Table 1. Chi-square correlation analysis showed that young (55.0% vs. 32.6%), female (47.8% vs. 31.2%), never smokers (46.8% vs. 28.9%), patients with adenocarcinoma histology (42.2% vs. 23.4%), and patients with an advanced stage of lung cancer (43.0% vs. 18.0%) were more likely to have BM (P < 0.05). The overall cumulative incidence of BM was significantly higher in the patients with mutated-EGFRs than those with WT-EGFR (51.6% vs. 27.3%, respectively; P < 0.001). In details, 53.1% of the exon 19 deletion-positive patients and 49.5% of the L858R point mutation-positive patients experienced BM during their entire disease course.
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| 100.0 |
NSCLC: non-small cell lung cancer; BM: brain metastases; EGFR: epidermal growth factor receptor; Mut: mutated; WT: wild type. The categorical data were presented as numbers (percentages) and the comparisons between groups used the chi-squared test. Non-adenocarcinoma group included squamous cell carcinoma, large cell carcinoma and NSCLC-not otherwise specified in this analysis. Uncommon mutations included 3 with an exon 18 mutation, 6 with an exon 20 insertion, and 1 with an exon 18 mutation and exon 20 insertion.
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study
| 99.94 |
The multivariable logistic regression analysis, as shown in Table 2, revealed that the presence of mutated-EGFR was significantly associated with a higher overall cumulative incidence of BM, as compared to that of WT-EGFR (odds ratio (OR) = 2.24, 95% confidence interval (CI), 1.37-3.64, P = 0.001) after adjusting for gender (not significant), age (OR = 2.44, 95% CI, 1.52-4.00, P < 0.001), smoking history (not significant), and stage at lung cancer diagnosis (OR = 4.02, 95% CI, 1.94-8.32, P < 0.001). In terms of the specific subtype of mutated-EGFRs, both the presence of exon 19 deletion and the presence of L858R point mutation were significantly associated with BM compared to the presence of WT-EGFR (OR = 2.18, 95% CI, 1.19β4.00, P = 0.012, and OR = 2.13, 95% CI, 1.23β3.75, P = 0.009, respectively); however, the difference between the exon 19 deletion-positive and the L858R point mutation-positive groups was not statistically significant (OR = 1.03, 95% CI, 0.54-1.94, P = 0.939).
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study
| 100.0 |
BM: brain metastases; EGFR: epidermal growth factor receptor; Mut: mutated; WT: wild type; OR: odds ratio; CI: confidence interval. Non-adenocarcinoma group included squamous cell carcinoma, large cell carcinoma and NSCLC-not otherwise specified in this analysis. # Uncommon mutation was not shown in the EGFR pairwise comparison due the small number of patients. In addition, the pairwise comparison was made in another multivariable logistic regression model. Β§Category after the slash (/) was set as reference category; * indicated significant at P < 0.0125 level in the multivariable model.
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study
| 99.94 |
To test whether a favorable overall survival (OS) influenced SBM in NSCLC patients who did not have BM at the diagnosis of lung cancer (n = 297), we correlated the length of OS with SBM occurrence. We found that the length of OS was associated with the cumulative incidence of SBM (P < 0.001), which strikingly increased from 1% (1/96) in all-stage patients with OS less than 6 months to 41.7% (35/84) in those with OS longer than 2 years (Figure 2A, upper). A similar surge of SBM was observed in the patients stratified from IIIB-IV NSCLC with OS longer than 2 years as compared to those with OS less than 6 months (Figure 2A, lower). KaplanβMeier analysis showed that EGFR-mutation status was associated with better survival outcomes in NSCLC (Figure 2B). To further determine whether the presence of mutated-EGFR predicted SBM, which is independent of the EGFR mutation-related better survival, we conducted a time-to-event analysis model considering death as a competing risk (Fine and Gray's sub-distribution hazard model) and found the cumulative incidence of SBM in the patients of all-stage NSCLC was 33.3% (45/135) in the mutated group and 11.1% (18/162) in the WT group, respectively (Hazard ratio (HR) = 3.0, 95% CI = 1.83-4.93, P < 0.001, Figure 2C left), and that in those of stage IIIB-IV NSCLC was 37.1% (39/105) in the mutated group and 10.6% (14/132) in the WT group, respectively (HR = 3.82, 95% CI = 2.07-7.06, P < 0.001, Figure 2C right). As to the stage I-IIIA patients primarily treated with surgery, the cumulative incidence of SBM between the mutated- and the WT-EGFR groups were not statistically different (25.0% (6/24) and 18.7% (3/16), respectively, P = 0.88, data not shown).
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study
| 100.0 |
(A) The length of overall survival (OS) and the cumulative incidence of SBM. (B) EGFR mutation status and OS. (C) EGFR mutation status and SBM. (D, E) Exon 19 deletion and L858R point mutation, and OS and SBM. Comparisons regarding OS and SBM were done using log-rank test and time-to-event data analysis considering death as a competing risk (β P) (Fine and Gray's sub-distribution hazard model). Note, M = month; Y = year; Mut = mutated; WT = wild-type.
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study
| 99.94 |
As to the comparison between the exon 19 deletion-positive and the L858R mutation-positive groups from stage IIIB-IV patients, there was a slightly longer median OS (20.6 vs.14.2 months, P of log-rank test = 0.368) in the former (Figure 2D), but no difference in the cumulative incidence of SBM (39.5% vs. 34.5%, HR= 1.12, 95% CI = 0.60-2.09, P = 0.720, Figure 2E) was observed between the two groups.
|
study
| 100.0 |
To confirm whether the presence of mutated-EGFR was independently associated with SBM, multivariable analysis was performed. For stage IIIB-IV NSCLC patients, the presence of mutated-EGFR was significantly associated with the occurrence of SBM as compared to that of WT-EGFR (HR = 2.98, 95% CI, 1.50-5.93, P = 0.002) after adjusting age (HR = 2.00, 95% CI =1.16-3.45, P = 0.012) and other common demographic covariates (Table 3). Similar results were observed for both the exon 19 deletion-positive and the L858R point mutation-positive groups when compared to the WT-EGFR group (HR = 2.79, 95% CI, 0.36-1.25, adjusted P = 0.012 and HR = 3.08, 95% CI, 0.33-1.49, P = 0.002, respectively). Further analysis revealed that there was no difference for SBM occurrence between the exon 19 deletion and L858R point mutation groups (HR = 0.91, 95% CI, 0.47β1.74, P = 0.770).
|
study
| 100.0 |
BM: brain metastases; NSCLC: non-small cell lung cancer; EGFR: epidermal growth factor receptor; Mut: mutated; WT: wild-type; HR: hazard ratio; CI: confidence interval. Non-adenocarcinoma group included squamous cell carcinoma, large cell carcinoma and NSCLC-not otherwise specified in this analysis. # Uncommon mutation was not shown in the EGFR pairwise comparison due to the small number of patients. In addition, the pairwise comparisons were made in another multivariable model. Β§ Category after the slash (/) was set as reference category; * indicated significant at P < 0.0125 level in the multivariable model. The association between the presence of mutated-EGFRs and subsequent BM was tested using a time-to-event analysis considering death as a competing risk (Fine and Gray's sub-distribution hazard model).
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study
| 100.0 |
To study the potential effect of the mutated-EGFRs on lung cancer progression, mutated EGFR [L858R (a point mutation in exon 21) or Del 3 (an in-frame deletion in exon 19)] or the wild-type (WT) one was introduced into H1437 (non-mutated) lung adenocarcinoma cells via lentiviral infection (Figure 3A). The ectopic expression of mutated- but not WT-EGFRs induced a morphological change from an epithelial phenotype to a spindle-like morphology (Figure 3B and Supplementary Figure 1A). Additionally, the electric cell-substrate impedance sensing (ECIS) analysis revealed that the mutated-EGFRs attenuated the impedance, indicating that the mutated-EGFRs inhibit barrier properties in lung cancer cells (Figure 3C). A wound healing assay showed that the mutated-EGFRs promoted cell migration, compared to the WT-EGFR (Figure 3D and Supplementary Figure 1B). In support of this notion, the cell-tracking assay showed that migration of H1437 cells were promoted by mutated-EGFRs but not the wild-type one (Figure 3E). Moreover, an endothelial cell-based invasion analysis was adopted to examine the metastatic potential of mutated-EGFR cells. We observed that H1437 cells carrying the mutated-EGFRs invaded more profoundly into the endothelial cells, thus attenuating the impedance of endothelial cells as compared to their wild-type counterparts (Figure 3F). Immunoblotting showed that the mutated-EGFRs not only elevated the levels of phosphorylated EGFR but also increased vimentin expression (Figure 3A), a hallmark of mesenchymal cells. To validate whether the mutated-EGFR promotes vimentin expression, we further conducted immunohistochemistry (IHC) staining on clinical tumor samples. Correlation analysis revealed that the EGFR-mutation status is associated with vimentin expression as compared to WT-EGFR (75.3% vs. 51.2%, P = 0.007) (Figure 3G). This finding was further supported by the analysis of two different lung adenocarcinoma cohorts (Figure 3H) (The raw materials were download from publicly accessible datasets) [14β15]. These data indicate that the mutated-EGFR promotes lung cancer cell dissemination and correlates with vimentin expression.
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study
| 100.0 |
(A) Western blot analysis of phosphorylated EGFR (p-EGFR), total EGFR (EGFR), vimentin (VIM) and GAPDH in H1437 cells infected with lentiviral vectors encoding wild-type (WT) and mutated-EGFRs (L858R, a point mutation in exon 21; Del 3, an in-frame deletion in exon 19 of EGFR tyrosine kinase domain) or an empty control vector (Ctrl). (B) Representative phase-contrast images of H1437 cells infected with lentiviral vectors encoding WT and mutated-EGFRs (L858R or Del 3) or empty control vector (magnification = 100X, scale bar = 100 ΞΌm). (C) Electric cell-substrate impedance sensing (ECIS) analysis to monitor the changes in cell impedance as a result of the EGFR functional responses in H1437 cells infected with lentiviral vectors encoding WT and mutated-EGFRs or an empty control vector. (D) Representative images of the wound healing assay for H1437 cells infected with lentiviral vectors encoding wild-type (WT) and mutated-EGFRs (L858R or Del 3) or the empty control (Ctrl) vector (upper). The dotted lines indicate the wound edge at 0, 24 and 48 hrs, respectively (magnification = 50X). Quantitative analysis for the cells migrated during 48 hours (lower) (student t-test). * indicated significant at P < 0.05. (E) Representative images of cell tracking assay for H1437 cells infected with lentiviral vectors encoding WT and mutated-EGFRs or an empty control vector (upper). The colored lines represented the individual tracks of the motile cells (magnification = 100X, scale bar = 100 ΞΌm). Quantitative analysis for cell tracking assay (lower) (student t-test). * indicated significant at P < 0.05, ** indicated significant at P < 0.01. (F) An ECIS assay to monitor the changes in cell impedance in HUVEC cells as a result of the invasion of H1437 cells infected with lentiviral vectors encoding WT and mutated-EGFRs or an empty control (Ctrl) vector. (G) Association between vimentin (VIM) expression and EGFR mutation status in patients with lung adenocarcinoma. Representative pictures of the immunohistochemical analysis of VIM expression in adenocarcinoma specimens. A VIM-negative, WT EGFR adenocarcinoma case (upper left) and a VIM-positive, mutated-EGFR (Mut) adenocarcinoma case (upper right) are shown. The pictures were scanned at x 40 magnification (scale bar = 100 ΞΌm) and the size was adjusted to the screen. The distribution of VIT expression in the lung cancer specimens from the mutated- and WT-EGFR groups was compared using Fisher's exact test (bottom). (H) Correlation analysis of VIM expression with EGFR mutation status in mutated- and WT EGFR lung adenoacrinomas (Chi-square test). The sources of VIM expression levels of lung cancer and the corresponding clinicopathological parameters were downloaded from Chitale et.al. Memorial Sloan-Kettering Cancer Center (http://cbio.mskcc.org/public/lung_array_data/) (Left) and TCGA (https://tcga-data.nci.nih.gov/docs/publications/luad_2014/) (Right).
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study
| 99.94 |
To determine whether lung tumors harboring mutated-EGFRs are more aggressive than those with WT-EGFR in terms of SBM occurrence, we used a median time interval between the diagnosis of lung cancer and the detection of SBM (MTSBM) as a surrogate of tumor aggressiveness. As shown in Table 4, the mutated-EGFR tumor had a significantly shorter MTSBM than the WT-EGFR one did (for all-stage disease, 31.6 months vs. not reached (NR), P of log-rank test = 0.043; for stage IIIB-IV disease, 23.5 months vs. NR, P = 0.017). As to stage IIIB-IV diseases with mutated-EGFRs, the L858R mutation-positive tumors had a slightly shorter MTSBM compared to the exon 19 deletion-positive ones (22.9 vs. 26.4 months, P = 0.743), but the difference was not statistically different.
|
study
| 100.0 |
MTSBM: median time interval between the diagnosis of lung cancer and the detection of subsequent brain metastases; BM: brain metastases; NSCLC: non-small cell lung cancer; SBM: subsequent BM; Patient no.: patient number; WT: wild-type; Mut: mutated; EGFR: epidermal growth factor receptor; NR: not reached. The MTSBM was estimated using the Kaplan- Meier method and group difference (i.e., EGFR mutations) was compared using log-rank tests.
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study
| 99.94 |
To determine whether EGFR-TKI treatment is associated with SBM, herein, we conducted a separate study. Of the patients without BM at the diagnosis of stage IIIB-IV NSCLC enrolled in Figure 2C right, 105 patients had mutated-EGFRs, 33 treated with EGFR-TKIs (TKI group) and 72 treated with non-TKI regimen (non-TKI group) as first-line treatment, respectively. More SBM was observed in TKI group (54.5%, 18/33) than in non-TKI group (29.2%, 21/72). As shown in Table 5, the administration of EGFR-TKIs as the 1st-line setting was associated with SBM (HR = 2.10, 95% CI = 1.15-3.82, P = 0.015) after adjusting for gender (HR = 2.38, 95% CI = 1.28-4.55, P = 0.007), age, smoking history and histological subtype.
|
study
| 99.94 |
EGFR: epidermal growth factor receptor; TKI: tyrosine kinase inhibitor; BM: brain metastasis; NSCLC: non-small cell lung cancer; HR: hazard ratio; CI: confidence interval. # The association between the administration of EGFR-TKI and subsequent BM was tested using a time-to-event analysis considering death as a competing risk (Fine and Gray's sub-distribution hazard model).
|
study
| 99.94 |
The present study showed that the presence of mutated-EGFRs not only was associated with overall BM but also predicted SBM in stage IIIB-IV NSCLC, irrespective of the length of patient OS. NSCLC harboring mutated-EGFRs displayed a higher vimentin expression and had a significantly shorter MTSBM as compared to those with WT-EGFR. As to the subtype of mutated-EGFRs, the exon 19 deletion-positive and the L858R point mutation-positive patient groups shared a similar cumulative incidence of SBM.
|
study
| 100.0 |
The association between mutated-EGFRs and BM from NSCLC has been reported before but their conclusions were not consistent [3β6, 16β18], which could result from the differences in patient number and selection, statistical methodology or interventional treatments. Notably, the mutated-EGFR lung tumors were reported to be more sensitive to both cytotoxic chemotherapy and EGFR-TKIs than the wild-type ones . Intriguingly, a better response to the treatment usually leads to a better disease control or a longer disease-free time interval at distant organs as well as a favorable survival; however, longer survival probably increases the risk of SBM development. Our analyses showed that a favorable OS was an important factor associated with SBM (P < 0.001, Figure 2A), which has been generally accepted and concerned, but was not clearly demonstrated in the previous reports [3β6, 16β18, 20, 21]. Notably, the rise of cumulative incidence curve of SBM was not apparent 3 years after the diagnosis of lung cancer (Figure 2C). Based on these results, the managements of SBM in NSCLC, including the prevention, early detection, and treatment, will become one of the main challenges for the patients who are expected to have a favorable survival, such as the mutated-EGFR group, especially during the first three-year follow-up.
|
study
| 99.94 |
We found that, independent of the survival factor, the presence of mutated-EGFRs was significantly associated with an increased risk of SBM in NSCLC as compared to those with WT-EGFR (HR = 2.98, P = 0.002). Similar results were recently reported by other research groups [4, 20, 21]. More importantly, we further observed that the lung tumors with mutated-EGFR progressed to the brain more rapidly than those with WT-EGFR in terms of MTSBM (23.5 months vs. NR, P = 0.017). These findings imply that the biological traits in cancer cells may contribute to SBM occurrence in NSCLC, however this possibility was rarely investigated in previous clinical reports. Prior in vitro experiments showed that the activation of EGFR upon ligand stimulation or by the mutation of EGFRvIII rather than EGFR overexpression correlates with cell migration and invasion in epithelial cancer cell lines, such as breast, oral squamous and glioblastoma cancers, and in NIH3T3 fibroblasts [11β13, 22]. Herein, we showed that the presence of mutated-EGFRs in lung cancer cells enhances cell mobility and promotes vimentin protein, a hallmark of mesenchymal cells . Obviously, in vitro data in the current study were not robust and had limitations to indicate the presence of epithelial-to-mesenchymal transition (EMT). However, the additional analyses of tumor samples from our and othersβ cohorts supported the correlation of EGFR-mutation status with vimentin expression, suggesting that EGFR-mutation status may be prone to undergo EMT-mediated cancer cell dissemination.
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study
| 100.0 |
The varied treatments, including EGFR-TKIs, may affect the occurrence of SBM in mutated-EGFR patients. Some pilot studies demonstrated that first generation of EGFR-TKIs therapy impacted the development of BM progression in advanced NSCLC [24β26]. However, this issue was not further investigated nor concluded in the recently published reports [4β6, 20, 21], possibly due to limitation of the primary goals and designs of their studies. Our result showed that first generation of EGFR-TKIs treatment as 1st setting is associated with SBM occurrence in mutated-EGFR patients (P = 0.015). One of the popular explanations for this phenomenon is that the discordance of drug concentration of EGFR-TKIs between in cerebrospinal fluid and in serum [27, 28], and the overall survival benefit of EGFR-TKIs provide chance and time for cancer cell colonization and proliferation in the brain, respectively. We acknowledged that the study population in Table 5 was small and highly selected, therefore large-scale studies are warranted to draw a firm conclusion in this issue. In addition, the authors also recognized that this finding could not be directly employed to the patients who receive third generation of EGFR TKIs (eg., Osimertinib, AZD3759), which has been reported to effectively penetrate the blood-brain barrier and display anti-tumor activity in the brain [29, 30].
|
study
| 99.9 |
Patients with an exon 19 deletion have longer survival compared to those with an L858R mutation [8β10], theoretically implying that more BM would be observed throughout the disease course of the former. One report supported this expectation (38.2% vs. 25.6%, P = 0.016) , but another and our data did not, regarding the overall BM in the patients of all-stage disease. Our analysis further showed that the cumulative incidence of SBM in stage IIIB-IV NSCLC was similar between the EGFR exon 19 deletion-positive and the L858R mutation-positive groups (39.5%, vs. 34.5%), although the former exhibited a slightly longer OS (20.6 vs. 14.2 months). This finding may be partially explained by the observations that the L858R mutation-positive tumors had an inferior disease control rate to EGFR-TKIs as first-line treatment (63.6% vs. 100%, P of chi-square test = 0.017, table not shown).
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study
| 100.0 |
One retrospective study suggested that a higher proportion of advanced mutated-EGFR NSCLC patients died of CNS metastases than did WT-EGFR patients (44.8% vs. 8.3%, P < 0.001) . Our findings that several factors contributed to SBM in NSCLC may be helpful in better understanding SBM occurrence and in clinical practice. Stage IIIB-IV NSCLC patients without BM at the time of lung cancer diagnosis were classified into subgroups by age and EGFR mutation status, and their cumulative incidences of SBM varied widely from 10.9 % (11/101) to 58.1% (18/31) (Figure 4), which indicates that NSCLC patients with mutated-EGFRs may require a higher frequency of brain imaging assessments than those with WT-EGFR to facilitate earlier BM detection, especially in the subgroup characterized by younger age and mutated-EGFRs (HR = 6.57, 95% CI = 3.17-13.70, P < 0.001).
|
study
| 99.94 |
There are several limitations in the current study. First is the nature of the retrospective study; patient selection, especially the lump of histological subtypes of NSCLC, is a potential bias. Our additional analyses targeting the lung adenocarcinoma patients showed the comparable results (Supplementary Tables 1 and 2). Moreover, a higher proportion of patients with adenocarcinoma histology received the EGFR testing compared to those with SCC (71.4% vs. 39.6%) is the second limitation; however this limitation implies that the influence of the presence of mutated-EGFRs on SBM occurrence compared to that of WT-EGFR had been possibly underestimated because patients with lung SCC have a smaller chance of harboring mutated-EGFRs (1-3%) and of experiencing BM than those with lung adenocarcinoma . The possibility of EGFR mutation discordance between the primary and metastatic sites may influence our results and represents another limitation. Based on the report indicating that the heterogeneous distribution of EGFR mutations is extremely rare in lung adenocarcinoma , we used the EGFR mutation status determined from primary or metastatic lung cancer specimens as a surrogate of the entire eligible population. Fourth, not all of the enrolled patients, such as those with early-stage disease, received intensively periodic brain imaging assessments after their NSCLC diagnosis. Furthermore, other driving oncogenes, such as KRAS and ALK mutations, were not factored into the analysis, largely because KRAS mutations were not common in our patient population (3.8%) and ALK rearrangements were not routinely tested during the study period. Moreover, because few cases had the T790M mutation (n = 5) in our study, we could not address the potential influence of T790M on the BM development. In addition, we recognized that our findings were limited to externally generalize to NSCLC patients who visited and received their major managements for lung cancer at our institutes, not to the Taiwan population. All the previously mentioned limitations may have influenced the clinical findings in the current study. To further elucidate this issue, large-scale studies cross populations are warranted.
|
study
| 99.94 |
In summary, we showed that several factors contributed to SBM occurrence in NSCLC. A favorable OS correlated to a higher frequency of SBM. In addition, the presence of mutated-EGFRs predicted an increased risk for SBM independent of age and other common covariates, and was associated with a shorter MTSBM in stage IIIB-IV NSCLC patients. Furthermore, the presence of an EGFR exon19 deletion and the presence of an L858R point mutation are comparable to predict subsequent BM. These results suggest NSCLC patients with mutated-EGFRs may require a higher frequency of brain imaging assessments than those with WT-EGFR to facilitate earlier SBM detection during follow-up.
|
study
| 99.94 |
Patients were selected from the lung cancer databases of Taipei Medical University Hospital (TMUH) and Wan Fang Hospital (WFH). Both TMUH, a teaching hospital, and WFH, a medical center, are run by Taipei Medical University. Patients were excluded if they had more than one primary cancer. Patients with stage I-IV NSCLC (including squamous cell carcinoma, adenocarcinoma, NSCLC-not otherwise specified and large cell carcinoma) that was histologically or cytologically confirmed between January 2006 and January 2012 (a total of 596, 382 cases from TMUH, 214 ones from WFH), and who had confirmed results from EGFR mutation testing were eligible for data collection by retrospective chart review (a total of 384, 195 cases from TMUH, 189 ones from WFH), with a data cutoff of August 2014 for outcome-SBM. This study was conducted with the approval of the Joint Institutional Review Board of Taipei Medical University (Approved number 201108006). Informed patient consent was obtained. The presence of BM was defined as previously described (Supplementary Materials and Methods). EGFR exon 18-21 mutations were determined using direct DNA sequencing, as previously described (Supplementary Materials and Methods). Patients with any or a combination of detectable EGFR exon 18-21 mutations, including common (exon 19 deletion and L858R point mutation), uncommon mutations (eg., exon 20 insertion, exon 18 mutation) and compound mutation (eg., exon 18/20), were placed into the mutated-EGFR group, and patients with no detectable mutated-EGFRs were put into the WT-EGFR group.
|
study
| 100.0 |
Human cell lines, including NCI-H1437 (ATCC CRL-5872), BEAS-2B (BCRC 60344) and HUVEC (BCRC H-UV001), were cultured for in vitro assays. The H1437 cells were kindly provided by Dr. Yu-Shan Chou at the Institute of Biomedical Sciences, Academia Sinica, Taiwan and further certified by the BCRC (Bioresource Collection and Research Center, Taiwan) through STR-PCR DNA profiling in 2014. The BEAS-2B cells were purchased from BCRC and certified via STR-PCR DNA profiling in 2017. The details of cell cultures, the plasmid construction, Q-PCR, and western blot analysis , wound healing and time-lapse cell tracking assays for the determination of cell motility conducted under the manufacturesβ instruction, electric cell-substrate impedance sensing (ECIS) assay for the determination of cell barrier function and invasion ability [38, 39], and IHC were presented in the supplementary material method section (Supplementary Materials and Methods).
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study
| 100.0 |
The characteristics of the BM and non-BM patients were compared using Chi-square tests. The association between EGFR mutations (mutated vs. WT) and overall BM (BM at the diagnosis of lung cancer and SBM) was determined using a multivariable logistic regression analysis. For those NSCLC patients without BM at the diagnosis of lung cancer, we tested the association between the presence of mutated-EGFR and SBM using a time-to-event analysis considering death as a competing risk (Fine and Gray's sub-distribution hazard model). To compare the exon 19, L858R and WT groups, we conducted a separate model (both logistic and time-to-event models) incorporating the details of EGFRs. Regarding the covariate selection, only the covariates that were significant (P < 0.05) in the univariate model were included in the multivariable model. In addition to analyzing the NSCLC patients of all-stage disease, we also performed a subgroup analysis that only included patients of stage IIIB-IV disease. Therefore, we performed multiple tests involving four comparisons for each outcome (overall BM in Table 2 and SBM in Table 3). To prevent the problem of type-I error inflation, we set the alpha level to 0.05/4 = 0.0125 in the multivariable model (Tables 2 and 3). In addition, we depicted OS using the Kaplan-Meier method and compared group differences (i.e., EGFR mutations) using log-rank tests. Finally, the distribution of vimentin expression in lung cancer specimens was categorized into a dichotomous variable (positive vs. negative), and the difference between the mutated- and WT-EGFR groups was compared using Fisher's exact test. Generally, P < 0.05 was considered as significant. Data analyses were conducted using SPSS 22 (Armonk, NY: IBM Corp) and R 3.1.3 (R Core Team, Vienna, Austria).
|
study
| 100.0 |
Establishing the etiology of respiratory tract infections (RTI) is often difficult due to the lack of a diagnostic gold standard and the inability to detect the causative pathogen. A large proportion of RTI is believed to be caused by respiratory viruses [1β6]. With widespread availability of molecular methods such as multiplex real-time polymerase chain reaction (rtPCR), clinical workflow has changed dramatically and the sensitivity of viral diagnostics has increased remarkably compared to conventional methods [3, 7β13]. However, the significance of virus detection remains unclear as the presence of a virus does not prove causality. Many respiratory viruses can be carried by asymptomatic children [4, 6, 14] and can be shed over prolonged periods, thus discrimination between carriage and infection is challenging [13β15]. Viral infection was reported previously to predispose to bacterial super-infection and concerns about possible bacterial co-infection remain [3, 7β13, 16β19]. Ruling out a bacterial infection with traditional microbiological techniques is frequently impossible [1, 5]. The predictive value of clinical signs to differentiate between viral and bacterial infection is also low [13, 17, 20β22]. On these grounds, clinical management of patients after respiratory virus diagnosis is controversial and surprisingly poorly studied. Overall, extensive yet often unnecessary use of antibiotics in RTI is common [1, 5, 6]. This adult and pediatric retrospective cohort study analyzed whether identification of a virus by multiplex rtPCR was associated with changes in the antibiotic treatment.
|
review
| 99.9 |
This was a retrospective cohort study of all pediatric and adult in- and outpatients in whom a 16-plex rtPCR assay for respiratory viruses was performed for upper and lower RTI, from either the Kantonsspital St. Gallen or Childrenβs hospital of Eastern Switzerland. Both hospitals are tertiary-care Swiss teaching hospitals with active infectious diseases consult services and easily accessible web-based local guidelines (www.guidelines.ch) for the treatment of community-acquired or hospital-acquired pneumonia. The guidelines are strongly recommended for use but not strictly reinforced, and include use of rtPCR as optional diagnostic in hospitalized patients, particularly with immune suppression. The study period was from September 2012 (when this assay was introduced) to November 2014. The documented application dates of anti-infective medication were matched with the date of rtPCR analysis in order to determine whether treatment was changed in response to rtPCR results. The main outcome of interest was whether antibiotic therapy was modified according to results of multiplex rtPCR. Secondary outcomes were prevalence and distribution of positive results of rtPCR, complications, length of stay (LOS), and antibiotic therapy depending on identified pathogens.
|
study
| 99.94 |
To identify patients, the database of the Centre for Laboratory Medicine was searched. Medical records were retrospectively analyzed to obtain basic demographic, clinical, laboratory and radiological parameters and data on clinical management. All chest radiographs (CXR) and computed tomographies (CT) for adults and children were reviewed by a pulmonologist and a pediatrician, respectively.
|
study
| 99.94 |
rtPCR results were available within 24 hours after testing. The application dates of anti-infective medication as documented in the medical records were correlated with the day of, or the day after, rtPCR analysis in order to define whether treatment initiation or discontinuation was associated with the results of viral testing.
|
study
| 99.94 |
The identified pathogens were retrospectively determined as relevant by an infectious disease specialist who integrated all available information. Etiologies were divided in four mutually exclusive groups: (i) bacterial (β₯1 bacteria); (ii) viral (β₯1 respiratory viruses); (iii) mixed (β₯1 bacteria and β₯1 respiratory viruses); or (iv) no pathogen (including fungi, non-respiratory virus, bacterial contaminant including coagulase-negative staphylococci, propionibacterium, corynebacterium, colonizing oral and respiratory flora). For some children, rapid detection tests (Alere BinaxNOW Influenza A&B, Quidel QuickVue RSV Test) for respiratory syncytial virus (RSV) and influenza A/B virus were available. These results were additionally considered in forming the different groups.
|
study
| 100.0 |
Management was considered correct for viral infections if there was no antibiotic treatment before and after rtPCR or antibiotics were stopped after positive rtPCR results became available; for bacterial or mixed infections, if antibiotics were given before and after rtPCR or were started after a negative rtPCR result. Patients with an indication other than RTI for antibiotic therapy were excluded. For patients with febrile neutropenia without a specific focus, the antibiotic indication was defined as βotherβ because antibiotics would usually not be stopped despite a viral detection. If a patient underwent repeated testing for respiratory viruses within 3 weeks, only the first positive result was counted. If the time interval was longer or the detected viruses diverged, a different episode was presumed and analyzed separately .
|
other
| 99.7 |
To reflect clinical decision making in real-life situations, sub-analyses were performed. Cases without detection of bacteria (i.e. patients with viral etiology or with no pathogen) were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobar or multilobar pulmonary infiltrate on CT or CXR; C-reactive protein (CRP) >100 mg/l; procalcitonin (PCT) >0.25 ΞΌg/l; antibiotic therapy before rtPCR and with indeterminate biomarkers (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP 51β100 mg/l and PCT not available). These criteria were adapted from earlier publications [17, 21] regarding the diagnosis of bacterial lower RTI.
|
study
| 100.0 |
The subgroup of patients with a viral etiology who had no clinically bacterial infection was considered to have a clinically viral infection. Children (<18 years) and adults (β₯18 years) were analyzed separately. Sepsis was defined according to standard criteria at the time . Systemic inflammatory response syndrome (SIRS) criteria for children were defined as age-specific .
|
study
| 99.94 |
For the imaging, if patients had interstitial infiltrates or ground glass opacities in the absence of unilobar or multilobar infiltrates, only therapy against βatypicalβ pathogens (macrolide, quinolone, tetracycline; but not antibiotics for coverage of βtypicalβ bacterial pathogens) was considered appropriate. If both CXR and CT were available, only CT readings were used for further analyses. An infiltrate was required for the diagnosis of pneumonia but no radiography was needed to diagnose a RTI in general.
|
other
| 99.9 |
The multiplex rtPCR was performed according to the manufacturerβs instruction (Seegene, Korea). The Anyplexβ’ II RV16 detection kit (Seegene, Korea) detects the following viruses: adenovirus, influenza A virus, influenza B virus, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus A/B/C, RSV A, RSV B, bocavirus 1/2/3/4, human metapneumovirus, coronavirus 229E, coronavirus NL63, coronavirus OC43, and enterovirus. Specimens that arrived before mid-morning from Monday to Friday were processed daily and results were provided by mid-afternoon. Specimens that arrived afterwards were processed on the following workday and reported by mid-afternoon. Dates of specimen collection and testing were available, but not date and time of reporting of results. For CRP, white blood cell count (WBC) and platelets, the most pathologic values within 3 days before and after rtPCR results were documented.
|
study
| 99.94 |
Quantitative variables are described as means Β± standard deviations or median and interquartile range (IQR), as appropriate. Qualitative variables are presented as absolute counts and relative percentages. Ο2-test or Fisherβs exact test were used to compare proportions, as appropriate. For continuous variables, the 2-sample independent t-test or the Mann-Whitney-U-test were used. P-values β€0.05 (2-sided) were considered statistically significant. Multivariate logistic regression was used to examine whether different predictors were associated with virus detection. Variables with a p-value β€0.05 in the univariate logistic regression were included. SPSS version 20.0 for Windows software, OpenEpi (www.openepi.com) and Microsoft Excel 2010 were used for statistical analyses.
|
study
| 99.94 |
rtPCR for respiratory viruses was performed on 328 respiratory specimens, of which 74 samples were excluded due to insufficient clinical information or repeated testing of separate specimens for respiratory viruses in the same patient within 3 weeks. Data on 254 patients were analyzed, including 11 sputa, 47 nasopharyngeal swabs, 63 nasopharyngeal aspirates, 123 bronchoalveolar lavages, 9 tracheal aspirates and 1 pleural effusion.
|
study
| 99.94 |
Baseline characteristics are presented in Tables 1, 2 and 3. One hundred and seven patients (42%) were female, and 72 were children (28%). Mean age in the group with viral infections was lower than in the remaining patients (29 vs. 47 years; p < 0.001) but the difference was not significant if children and adults were analyzed separately (children 4.3 vs. 5.7 years; p = 0.28; adults 53.6 vs. 56.6 years; p = 0.31). There were more patients with neutropenia, hematological malignancy or collagen vascular disease/vasculitis in the viral group (p < 0.001; p = 0.04; p = 0.01). Diagnosis of bronchitis and upper RTI were more common in the viral group (p = 0.02; p = 0.004).Table 1Baseline characteristics for adult patients Missing Total Viral a Any virus b Other c p-value d values (n = 182) (n = 40) (n = 46) (n = 142) Viral vs. any virus Viral vs. other Demographics Age, mean years Β± SD (range)55.9 Β± 16.1 (18β88)53.6 Β± 16.1 (18β83)53.9 Β± 15.9 (18β83)56.6 Β± 16.1 (18β88)0.930.30 Female sex, n (%)76 (41.8)14 (35.0)19 (41.3)62 (43.7)0.550.33 Outpatients, n (%)20 (11.0)5 (12.5)5 (10.9)15 (10.6)1.000.92Comorbidities, n (%) Asthma13 (7.1)2 (5.0)4 (8.7)11 (7.7)0.810.85 COPD27 (10.6)5 (12.5)7 (15.2)22 (15.5)0.720.64 Other chronic lung diseasee 26 (14.3)2 (5.0)2 (4.3)24 (16.9)1.000.06 Solid cancerf 25 (13.7)3 (7.5)3 (6.5)22 (15.5)1.000.20 Hematologic malignancy38 (20.9)13 (32.5)15 (32.6)25 (17.6)0.990.04 Organ transplantation13 (7.1)3 (7.5)3 (6.5)10 (7.0)1.001.00 Neutropenia20 (11.0)9 (22.5)9 (19.6)11 (7.7)0.740.03 HIV infection6 (3.3)1 (2.5)2 (4.3)5 (3.5)1.001.00 Diabetes mellitus27 (14.8)6 (15.0)7 (15.2)21 (14.8)0.980.97 Collagen vascular disease/Vasculitis33 (18.1)4 (10.0)5 (10.9)29 (20.4)1.000.13 Systemic steroids49 (26.9)11 (27.5)14 (30.4)38 (26.8)0.770.93 Other Immunosuppressiong 21 (11.5)5 (12.5)6 (13.0)16 (11.3)0.941.00 Chronic renal failure45 (24.7)11 (27.5)13 (28.3)34 (23.9)0.940.65Clinical findings Systolic blood pressure, mmHg, mean Β± SD (range)9125 Β± 24 (63β207)129 Β± 27 (63β207)128 Β± 28 (63β207)123 Β± 22 (67β197)0.870.17 Heart rate, beats/min, mean Β± SD (range)894 Β± 20 (51β155)91 Β± 19 (51β150)94 Β± 19 (51β150)94 Β± 20 (56β155)0.470.40 Respiratory rate, breaths/min, mean Β± SD (range)13026 Β± 9 (10β60)23 Β± 8 (12β36)27 Β± 13 (12β60)27 Β± 10 (10β60)0.390.23 Body temperature, Β°C, mean Β± SD (range)2037.6 Β± 1.0 (35.4β42.0)37.5 Β± 0.9 (35.6β39.6)37.5 Β± 0.9 (35.6β39.6)37.6 Β± 1.0 (35.4β42.0)1.000.59Laboratory findingsh, mean Β± SD (range) C-reactive protein (maximum), mg/l13151 Β± 127 (1β500)159 Β± 148 (1β500)166 Β± 152 (1β500)148 Β± 121 (1β499)0.830.64 White blood cells (maximum), G/l1111.5 Β± 10.2 (0.0β97.0)12.2 Β± 16.8 (1.8β97.0)12.6 Β± 16.3 (1.8β97.0)11.3 Β± 7.3 (0.0β41.1)0.910.75 Platelets (minimum), G/l11202 Β± 128 (4β713)159 Β± 117 (5β513)165 Β± 117 (5β513)215 Β± 129 (4β713)0.820.02Discharge diagnosis, n (%) Bronchitis22 (12.1)7 (17.5)7 (15.2)15 (10.6)0.780.36 Acute exacerbation of COPD5 (2.7)1 (2.5)1 (2.2)4 (2.8)1.001.00 Upper respiratory tract infection8 (4.4)4 (10.0)4 (8.7)4 (2.8)1.000.14 Respiratory tract infection, unspecified7 (3.8)2 (5.0)4 (8.7)5 (3.5)0.810.96 Community-acquired pneumonia65 (35.7)21 (52.5)25 (54.3)44 (31.0)0.860.01 Hospital-acquired pneumonia12 (6.6)0 (0.0)0 (0.0)12 (8.5) n/a 0.09 Aspiration pneumonia1 (0.5)0 (0.0)0 (0.0)1 (0.7) n/a 1.00 Tuberculosis3 (1.6)0 (0.0)0 (0.0)3 (2.1) n/a 0.95 Otheri 59 (32.4)5 (12.5)5 (10.9)54 (38.0)1.000.002Β°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation aCases in which only one or more respiratory viruses were detected bCases in which one or more respiratory viruses were detected (as single or mixed infection) cIncludes bacterial etiology, mixed etiology, no pathogen dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension fAll solid tumors including bronchial carcinoma gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR iOther infections (n = 10); neoplastic diseases (n =6); collagen vascular; other rheumatologic or autoimmune (n = 14); sarcoidosis (n = 3); non-infectious non-neoplastic pulmonary diseases (n = 23); cardiovascular diseases (n = 3) Table 2Baseline characteristics for pediatric patients Missing Total Viral a Any virus b Other c p-value d values (n = 72) (n = 40) (n = 45) (n = 32) Viral vs. any virus Viral vs. other Demographics Age, mean years Β± SD (range)4.9 Β± 5.7 (0β17)4.3 Β± 5.4 (0β16)4.7 Β± 5.5 (0β16)5.7 Β± 6.0 (0β17)0.740.30 Female sex, n (%)31 (43.1)14 (35.0)18 (40.0)17 (53.1)0.640.13 Outpatients, n (%)3 (4.2)2 (5.0)2 (4.4)1 (3.1)1.001.00Comorbidities, n (%) Asthma1 (1.4)1 (2.5)1 (2.2)0 (0.0)1.001.00 Other chronic lung diseasee 13 (18.1)7 (17.5)8 (17.8)6 (18.8)0.970.89 Solid cancerf 1 (1.4)0 (0.0)0 (0.0)1 (3.1) n/a 0.89 Haematologic malignancy10 (13.9)8 (20.0)9 (20.0)2 (6.3)1.000.18 Organ transplantation1 (1.4)1 (2.5)1 (2.2)0 (0.0)1.001.00 Neutropenia9 (12.5)8 (20.0)8 (17.8)1 (3.1)0.790.06 Systemic steroids8 (11.1)5 (12.5)6 (13.3)3 (9.4)0.910.98 Other Immunosuppressiong 3 (4.2)3 (7.5)3 (6.7)0 (0.0)1.000.33Clinical findings Systolic blood pressure, mmHg, mean Β± SD (range)29100 Β± 18 (59β140)106 Β± 15 (71β140)105 Β± 14 (71β140)95 Β± 18 (59β120)0.820.04 Heart rate, beats/min, mean Β± SD (range)3136 Β± 33 (60β234)138 Β± 32 (60β186)134 Β± 32 (60β186)135 Β± 35 (72β234)0.580.71 Respiratory rate, breaths/min, mean Β± SD (range)1541 Β± 20 (16β103)41 Β± 21 (18β103)40 Β± 21 (16β103)40 Β± 19 (16β88)0.840.86 Body temperature, Β°C, mean Β± SD (range)337.6 Β± 1.1 (35.0β40.1)37.5 Β± 1.1 (35.0β39.5)37.5 Β± 1.1 (35.0β39.5)37.7 Β± 1.1 (35.1β40.1)1.000.46Laboratory findingsh, mean Β± SD (range) C-reactive protein (maximum), mg/l285 Β± 141 (5β999)62 Β± 77 (5β291)67 Β± 81 (5β293)113 Β± 191 (7β999)0.780.16 White blood cells (maximum), G/l216.0 Β± 12.1 (0.2β63.1)12.6 Β± 10.0 (0.2β57.0)13.6 Β± 11.3 (0.2β57.0)20.1 Β± 13.3 (1.8β63.1)0.680.01 Platelets (minimum), G/l2246 Β± 144 (15β674)257 Β± 175 (15β674)244 Β± 169 (15β674)234 Β± 96 (16β488)0.730.49Discharge diagnosis, n (%) Bronchitis10 (13.9)9 (22.5)9 (20.0)1 (3.1)0.780.04 Upper respiratory tract infection14 (19.4)9 (22.5)10 (22.2)5 (15.6)0.980.47 Respiratory tract infection, unspecified4 (5.6)4 (10.0)4 (8.9)0 (0.0)1.000.18 Community-acquired pneumonia15 (20.8)6 (15.0)8 (17.8)9 (28.1)0.730.18 Hospital-acquired pneumonia10 (13.9)5 (12.5)6 (13.3)5 (15.6)0.910.96 Aspiration pneumonia2 (2.8)1 (2.5)2 (4.4)1 (3.1)1.001.00 Otheri 17 (23.6)6 (15.0)6 (13.3)11 (34.4)0.830.06Β°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation aCases in which only one or more respiratory viruses were detected bCases in which one or more respiratory viruses were detected (as single or mixed infection) cIncludes bacterial etiology, mixed etiology, no pathogen dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension fAll solid tumors including bronchial carcinoma gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR iOther infections (n = 14); neoplastic diseases (n = 1); collagen vascular; other rheumatologic or autoimmune (n = 1); gastroesophageal diseases (n = 1) Table 3Baseline characteristics for all patients Missing Total Viral a Any virus b Other c p-value d values (n = 254) (n = 80) (n = 91) (n = 174) Viral vs. any virus Viral vs. other Demographics Age, mean years Β± SD (range)41.5 Β± 26.9 (0β88)29.0 Β± 27.5 (0β83)29.6 Β± 27.4 (0β83)47.2 Β± 24.7 (0β88)0.89<0.001 Female sex, n (%)107 (42.1)28 (35.0)37 (40.7)79 (45.4)0.450.12 Children, n (%)72 (28.3)40 (50.0)45 (49.5)32 (18.4)0.94<0.001 Outpatients, n (%)23 (9.1)7 (8.8)7 (7.7)16 (9.2)0.800.91Comorbidities, n (%) Asthma14 (5.5)3 (3.8)5 (5.5)11 (6.3)0.870.61 COPD27 (10.6)5 (6.3)7 (7.7)22 (12.6)0.710.13 Other chronic lung diseasee 39 (15.4)9 (11.3)10 (11.0)30 (17.2)0.960.22 Solid cancerf 26 (10.2)3 (3.8)3 (3.3)23 (13.2)1.000.02 Haematologic malignancy48 (18.9)21 (26.3)24 (26.4)27 (15.5)0.990.04 Organ transplantation14 (5.5)4 (5.0)4 (4.4)10 (5.7)1.001.00 Neutropenia29 (11.4)17 (21.3)17 (18.7)12 (6.9)0.68<0.001 HIV infection6 (2.4)1 (1.3)2 (2.2)5 (2.9)1.000.77 Diabetes mellitus27 (10.6)6 (7.5)7 (7.7)21 (12.1)0.960.28 Collagen vascular disease/Vasculitis33 (13.0)4 (5.0)5 (5.5)29 (16.7)1.000.01 Systemic steroids57 (22.4)16 (20.0)20 (22.0)41 (23.6)0.750.53 Other Immunosuppressiong 24 (9.4)8 (10.0)9 (9.9)16 (9.2)0.980.84 Chronic renal failure45 (17.7)11 (13.8)13 (14.3)34 (19.5)0.920.26Clinical findings Systolic blood pressure, mmHg, mean Β± SD (range)38120 Β± 25 (59β207)121 Β± 26 (63β207)119 Β± 26 (63β207)119 Β± 24 (59β197)0.670.60 Heart rate, beats/min, mean Β± SD (range)11106 Β± 31 (51β234)114 Β± 35 (51β186)114 Β± 33 (51β186)102 Β± 28 (56β234)1.000.01 Respiratory rate, breaths/min, mean Β± SD (range)14534 Β± 18 (10β103)37 Β± 21 (12β103)37 Β± 20 (12β103)32 Β± 15 (10β88)1.000.17 Body temperature, Β°C, mean Β± SD (range)2337.6 Β± 1.0 (35.0β42.0)37.5 Β± 1.0 (35.0β39.6)37.5 Β± 1.0 (35.0β39.6)37.6 Β± 1.0 (35.1β42.0)1.000.48Laboratory findingsh, mean Β± SD (range) C-reactive protein (maximum), mg/l15132 Β± 134 (1β999)111 Β± 127 (1β500)117 Β± 132 (1β500)141 Β± 137 (1β999)0.770.11 White blood cells (maximum), G/l1312.8 Β± 11.0 (0.0β97.0)12.4 Β± 13.8 (0.2β97.0)13.1 Β± 14.0 (0.2β97.0)13.1 Β± 9.4 (0.0β63.1)0.750.69 Platelets (minimum), G/l13215 Β± 134 (4β713)208 Β± 156 (5β674)204 Β± 149 (5β674)218 Β± 123 (4β713)0.870.62Discharge diagnosis, n (%) Bronchitis32 (12.6)16 (20.0)16 (17.6)16 (9.2)0.690.02 Acute exacerbation of COPD5 (2.0)1 (1.3)1 (1.1)4 (2.3)1.000.99 Upper respiratory tract infection22 (8.7)13 (16.3)14 (15.4)9 (5.2)0.880.004 Respiratory tract infection, unspecified11 (4.3)6 (7.5)8 (8.8)5 (2.9)0.760.18 Community-acquired pneumonia80 (31.5)27 (33.8)33 (36.3)53 (30.5)0.730.60 Hospital-acquired pneumonia22 (8.7)5 (6.3)6 (6.6)17 (9.8)0.930.36 Aspiration pneumonia3 (1.2)1 (1.3)2 (2.2)2 (1.1)1.001.00 Tuberculosis3 (1.2)0 (0.0)0 (0.0)3 (1.7)n/a0.64 Otheri 76 (29.9)11 (13.8)11 (12.1)65 (37.4)0.75<0.001Β°C, degree Celsius, COPD chronic obstructive pulmonary disease, HIV human immunodeficiency virus, n number, SD standard deviation aCases in which only one or more respiratory viruses were detected bCases in which one or more respiratory viruses were detected (as single or mixed infection) cIncludes bacterial etiology, mixed etiology, no pathogen dFor continuous variables, 2-sample independent t-test was used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used eOther chronic lung diseases, e.g. cystic fibrosis, pulmonary sarcoidosis, pulmonary hypertension fAll solid tumors including bronchial carcinoma gPatients with one of the following conditions: primary or secondary antibody deficiency, congenital immunodeficiency, immunosuppressive therapy other than steroids, severe malnutrition with cachexia hHighest/lowest value within a time period of 3 days before and 3 days after date of rtPCR iOther infections (n = 24); neoplastic diseases (n = 7); collagen vascular; other rheumatologic or autoimmune (n = 15); sarcoidosis (n = 3); non-infectious non-neoplastic pulmonary diseases (n = 23); cardiovascular diseases (n = 3); gastroesophageal diseases (n = 1)
|
study
| 99.94 |
iOther infections (n = 24); neoplastic diseases (n = 7); collagen vascular; other rheumatologic or autoimmune (n = 15); sarcoidosis (n = 3); non-infectious non-neoplastic pulmonary diseases (n = 23); cardiovascular diseases (n = 3); gastroesophageal diseases (n = 1)
|
other
| 99.94 |
Any pathogen was identified in 140 patients (55%), in 89 of 182 adults (49%) and in 51 of 72 children (71%). Among these patients, one or more respiratory virus was detected in 91 (65%), one or more bacteria in 53 (38%) and a mixed viral-bacterial infection in 11 (8%) patients. 45 of 72 children (63%) were infected with one or more respiratory viruses. Compared to children, viral detection in adults was less frequent (25%, n = 46; p < 0.001). A single pathogen was identified in 99 patients (39%); multiple pathogens were detected in 41 patients (16%). Distribution of detected pathogens and the differences between children and adults are shown in Table 4, and Figs. 1, 2a and b.Table 4Relevant pathogens identified from respiratory specimens Total (n = 254) Adults (n = 182) Children (n = 72) Bacteria, n (%)66 (26.0)54 (29.7)12 (16.7) Haemophilus influenzae 12 (4.7)11 (6.0)1 (1.4) Klebsiella pneumoniae 8 (3.1)6 (3.3)2 (2.8) Staphylococcus aureus 4 (1.6)1 (0.5)3 (4.2) Escherichia coli 4 (1.6)3 (1.6)1 (1.4) Pseudomonas aeruginosa 4 (1.6)4 (2.2)0 (0.0) Streptococcus pneumoniae 3 (1.2)2 (1.1)1 (1.4) Streptococcus pyogenes 3 (1.2)2 (1.1)1 (1.4) Legionella pneumophila 3 (1.2)3 (1.6)0 (0.0) Mycobacterium tuberculosis 3 (1.2)3 (1.6)0 (0.0) Mycoplasma pneumoniae 1 (0.4)0 (0.0)1 (1.4) Other bacteria21 (8.3)19 (10.4)2 (2.8)Viruses, n (%)119 (46.9)54 (29.7)65 (90.3) Rhinovirus A/B/C33 (13.0)16 (8.8)17 (23.6) Influenza A virus17 (6.7)11 (6.0)6 (8.3) Influenza B virus4 (1.6)0 (0.0)4 (5.6) Adenovirus14 (5.5)4 (2.2)10 (13.9) Bocavirus 1/2/3/49 (3.5)0 (0.0)9 (12.5) Respiratory syncytial virus A8 (3.1)4 (2.2)4 (5.6) Respiratory syncytial virus B6 (2.4)5 (2.7)1 (1.4) Parainfluenza virus 11 (0.4)1 (0.5)0 (0.0) Parainfluenza virus 21 (0.4)0 (0.0)1 (1.4) Parainfluenza virus 36 (2.4)3 (1.6)3 (4.2) Parainfluenza virus 45 (2.0)2 (1.1)3 (4.2) Human Metapneumovirus5 (2.0)2 (1.1)3 (4.2) Enterovirus3 (1.2)0 (0.0)3 (4.2) Coronavirus 229E1 (0.4)1 (0.5)0 (0.0) Coronavirus NL632 (0.8)1 (0.5)1 (1.4) Coronavirus OC431 (0.4)1 (0.5)0 (0.0) Non respiratory viruses3 (1.2)3 (1.6)0 (0.0)Fungi, n (%)10 (3.9)9 (4.9)1 (1.4) Pneumocystis jirovecii6 (2.4)6 (3.3)0 (0.0) Other fungi4 (1.6)3 (1.6)1 (1.4)Pathogens associated with mixed infections were counted individually Fig. 1Distribution of respiratory viruses detected as single or mixed pathogen Fig. 2 a Distribution of identified pathogens for adults. b Distribution of identified pathogens for children
|
study
| 99.94 |
Of the 254 patients in the cohort, 61 (24%) received antibiotics before hospitalization, and 149 (59%) of all in- and outpatients received antibiotics at the time of rtPCR testing. Of 80 patients with a viral etiology, 59 (74%) received antibiotics at any time point, 28 of 40 children (70%) and 31 of 40 adults (78%). Inpatients with a bacterial etiology were treated with antibiotics in 92% (p = 0.09) and longer than those with a viral etiology or no pathogen (p = 0.02; p = 0.01). If children and adults were analyzed individually, similar but non-significant trends were observed (Tables 5, 6 and 7).Table 5Outcome depending on relevant detected pathogen for adult patients Viral Bacterial Mixed No pathogen p-value a (n = 40) (n = 36) (n = 6) (n = 100) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen LOS inpatients, median days (IQR)8 (6β21)21 (13β35)11.5 (5β44.25)15 (8β23.5)<0.0010.670.03 Complications, n (%) ICU admission11 (27.5)13 (36.1)3 (50.0)24 (24.0)0.420.510.67 Mechanical ventilation6 (15.0)11 (30.6)3 (50.0)19 (19.0)0.110.160.58 ARDS3 (7.5)5 (13.9)2 (33.3)6 (6.0)0.600.241.00 Sepsis24 (60.0)24 (66.7)5 (83.3)6 (6.0)b 0.550.53n/a Mortality (all cause)4 (10.0)4 (11.1)1 (16.7)6 (6.0)1.001.000.62 Antibiotic use (any indication) Any inpatient antibiotics, n (%)30/35 (85.7)29/32 (90.6)4/6 (66.7)72/89 (80.9)0.810.540.53 Duration of inpatient use, mean days Β± SD (range)12.5 Β± 14.3 (0β63)18.1 Β± 16.0 (0β72)10.3 Β± 12.1 (0β31)10.8 Β± 11.4 (0β63)0.140.730.49 Discharged receiving oral antibiotics, n (%)11 (30.6)c 17 (53.1)d 1 (20.0)e 23 (24.5)f 0.061.000.48 ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used bSepsis requires a pathogen per definition. In these six cases sepsis was exceptionally defined according to discharge papersMissing values due to death or ongoing hospitalisation at time of analysis (number): c4; d4; e1; f6. For calculation of percentage and p-value missing values were excluded Table 6Outcome depending on relevant detected pathogen for pediatric patients Viral Bacterial Mixed No pathogen p-value a (n = 40) (n = 6) (n = 5) (n = 21) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen LOS inpatients, median days (IQR)18.5 (6β48.75)47.5 (14β95.75)34 (17.5β201.5)37 (8β70)0.190.100.45 Complications, n (%) ICU admission18 (45.0)4 (66.7)5 (100.0)12 (57.1)0.580.060.37 Mechanical ventilation8 (20.0)4 (66.7)4 (80.0)11 (52.4)0.070.030.01 ARDS1 (2.5)0 (0.0)1 (20.0)0 (0.0)1.000.421.00 Sepsis17 (42.5)4 (66.7)2 (40.0)0 (0.0)0.501.00n/a Mortality (all cause)2 (5.0)0 (0.0)0 (0.0)0 (0.0)1.001.000.85 Antibiotic use (any indication) Any inpatient antibiotics, n (%)28/38 (73.7)6/6 (100.0)5/5 (100.0)18/20 (90.0)0.380.490.26 Duration of inpatient use, mean days Β± SD (range)8.6 Β± 13.4 (0β73)14.2 Β± 11.0 (0β34)13.8 Β± 7.8 (7β24)6.2 Β± 4.8 (0β18)0.340.400.33 Discharged receiving oral antibiotics, n (%)6 (15.8)b 0 (0.0)1 (20.0)3 (15.0)c 0.781.001.00 ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were usedMissing values due to death or ongoing hospitalisation at time of analysis (number): b2; c1. For calculation of percentage and p-value missing values were excluded Table 7Outcome depending on relevant detected pathogen for all patients Viral Bacterial Mixed No pathogen p-value a (n = 80) (n = 42) (n = 11) (n = 121) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen LOS inpatients, median days (IQR)12 (6β25.5)22 (13β42.5)27 (8β72)16 (8β29.25)0.0040.200.20 Complications, n (%) ICU admission29 (36.3)17 (40.5)8 (72.7)36 (29.8)0.650.050.34 Mechanical ventilation14 (17.5)15 (35.7)7 (63.6)30 (24.8)0.030.010.22 ARDS4 (5.0)5 (11.9)3 (27.3)6 (5.0)0.310.071.00 Sepsis41 (51.3)28 (66.7)7 (63.6)6 (5.0)b 0.100.44n/a Mortality (all cause)6 (7.5)4 (9.5)1 (9.1)6 (5.0)0.941.000.65 Antibiotic use (any indication) Any inpatient antibiotics, n (%)58/73 (79.5)35/38 (92.1)9/11 (81.8)90/109 (82.6)0.091.000.60 Duration of inpatient use, mean days Β± SD (range)10.5 Β± 13.9 (0-73)17.5 Β± 15.3 (0β72)11.9 Β± 10.0 (0β31)10.0 Β± 10.6 (0β63)0.020.750.80 Discharged receiving oral antibiotics, n (%)17 (23.0)c 17 (44.7)d 2 (20.0)e 26 (22.8)f 0.021.000.98 ARDS acute respiratory distress syndrome, ICU intensive care unit, IQR interquartile range, LOS length of stay, n number, SD standard deviation aFor continuous variables, 2-sample independent t-test or Mann-Whitney-U-test were used. For categorical variables, Mantel-Haenszel chi square or Fisher exact test were used bSepsis requires a pathogen per definition. In these six cases sepsis was exceptionally defined according to discharge papersMissing values due to death or ongoing hospitalisation at time of analysis (number): c6; d4; e1; f7. For calculation of percentage and p-value missing values were excluded
|
study
| 99.94 |
The effect of rtPCR analysis on antibiotic management is presented in Tables 8, 9 and 10. After exclusion of patients who received antibiotics for other indications virus detection was temporally associated with discontinuation of antibiotics in 2 of 20 adults (10%) and 6 of 14 children (43%). In patients with viral etiology, management was more frequently judged correct in children (18/27, 67%) than in adults (12/35, 34%; p = 0.01) after rtPCR results became available. In adults, management of viral etiology was less often judged correct compared to adults with bacterial etiology (p = 0.002). Among patients with clinically viral etiology, children were more frequently managed correctly (15/15, 100%) than adults (8/13, 62%; p = 0.03).Table 8Change of antibiotic therapy after rtPCR, adult patients with another indication for antibiotics were excluded Viral Bacterial Mixed No pathogen Clinically Clinically p-value c (n = 35) (n = 33) (n = 6) (n = 84) bacterial a (n = 84) viral b (n = 13) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen No antibiotic treatment before and after rtPCR, n (%) 10 (28.6) 7 (21.2)2 (33.3)32 (38.1)18 (21.4) 8 (61.5) 0.491.000.32Antibiotic treatment stopped after rtPCR, n (%) 2 (5.7) 2 (6.1)0 (0.0)2 (2.4)4 (4.8) 0 (0.0) 1.001.000.67Antibiotic treatment started after rtPCR, n (%)5 (14.3) 4 (12.1) 2 (33.3) 8 (9.5) 7 (8.3) 3 (23.1)1.000.540.64Antibiotic treatment before and after rtPCR, n (%)18 (51.4) 20 (60.6) 2 (33.3) 42 (50.0) 55 (65.5) 2 (15.4)0.450.710.89Correct management, n (%) 12 (34.3) 24 (72.7) 4 (66.7) 62 (73.8) 8 (61.5) 0.002 0.30n/a n number; rtPCR, real-time polymerase chain reaction aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available) bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above) cMantel-Haenszel chi square test or Fisher exact test were used Table 9Change of antibiotic therapy after rtPCR, pediatric patients with another indication for antibiotics were excluded Viral Bacterial Mixed No pathogen Clinically Clinically p-value c (n = 27) (n = 4) (n = 3) (n = 18) bacterial a (n = 22) viral b (n = 15) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen No antibiotic treatment before and after rtPCR, n (%) 12 (44.4) 1 (25.0)0 (0.0)6 (33.3)6 (27.3) 11 (73.3) 0.870.400.46Antibiotic treatment stopped after rtPCR, n (%) 6 (22.2) 0 (0.0)0 (0.0)1 (5.6)2 (9.1) 4 (26.7) 0.801.000.27Antibiotic treatment started after rtPCR, n (%)1 (3.7) 0 (0.0) 1 (33.3) 3 (16.7) 3 (13.6) 0 (0.0)1.000.390.34Antibiotic treatment before and after rtPCR, n (%)8 (29.6) 3 (75.0) 2 (66.7) 8 (44.4) 11 (50.0) 0 (0.0)0.230.500.32Correct management, n (%) 18 (66.7) 3 (75.0) 3 (100.0) 14 (63.6) 15 (100.0) 1.000.66n/a n number; rtPCR, real-time polymerase chain reaction aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available) bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above) cMantel-Haenszel chi square test or Fisher exact test were used Table 10Change of antibiotic therapy after rtPCR, all patients with another indication for antibiotics were excluded Viral Bacterial Mixed No pathogen Clinically Clinically p-value c (n = 62) (n = 37) (n = 9) (n = 102) bacterial a (n = 106) viral b (n = 28) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen No antibiotic treatment before and after rtPCR, n (%) 22 (35.5) 8 (21.6)2 (22.2)38 (37.3)24 (22.6) 19 (67.9) 0.150.710.82Antibiotic treatment stopped after rtPCR, n (%) 8 (12.9) 2 (5.4)0 (0.0)3 (2.9)6 (5.7) 4 (14.3) 0.400.640.03Antibiotic treatment started after rtPCR, n (%)6 (9.7) 4 (10.8) 3 (33.3) 11 (10.8) 10 (9.4) 3 (10.7)1.000.160.82Antibiotic treatment before and after rtPCR, n (%)26 (41.9) 23 (62.2) 4 (44.4) 50 (49.0) 66 (62.3) 2 (7.1)0.051.000.38Correct management, n (%) 30 (48.4) 27 (73.0) 7 (77.7) 76 (71.7) 23 (82.1) 0.020.19n/a n number; rtPCR, real-time polymerase chain reaction aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available) bCases with a detected viral pathogen excluding those patients with a clinically bacterial co-infection (as described above) cMantel-Haenszel chi square test or Fisher exact test were used
|
study
| 99.94 |
aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available)
|
study
| 96.75 |
aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available)
|
study
| 96.75 |
aCases without detection of bacteria were evaluated as clinically bacterial if they fulfilled one of the following criteria: unilobular or multilobular pulmonary infiltrate or CRP >100 mg/l or PCT >0.25 ΞΌg/l or antibiotic therapy before rtPCR and no bacterium detection and biomarkers indeterminate (CRP >100 mg/l and PCT β€0.25 ΞΌg/l or CRP between 51 and 100 mg/l and PCT not available)
|
study
| 96.75 |
Eight adults and one child received oseltamivir. In four of five patients with proven influenza A virus infection, the antiviral medication was prescribed in response to the positive rtPCR analysis. In another child, oseltamivir was commenced after the third successive detection of influenza A virus within a month and stopped after 1 day. In two other patients, antiviral therapy was started or continued despite an rtPCR analysis negative for influenza and positive for other respiratory viruses. In another patient with identification of only bacterial pathogens, oseltamivir was stopped after negative rtPCR results were available. In an additional case with detection of bacteria only, antiviral medication was started 3 days after rtPCR analysis and it was stopped again on the next day.
|
clinical case
| 98.1 |
Hospital length of stay (LOS) was longer in patients with bacterial etiology compared to patients with a viral etiology. For children, LOS did not significantly vary in the different groups between viral and bacterial etiologies (Tables 5, 6 and 7). Patients with a mixed infection were more frequently admitted to the intensive care unit (ICU) and mechanically ventilated compared to patients with a viral etiology (p = 0.05; p = 0.005; respectively). If children and adults were analyzed separately, the differences within the adult population were not significant; in children, more patients with a mixed infection were mechanically ventilated (p = 0.03). All-cause and RTI-associated mortality was comparable between pathogen groups.
|
study
| 99.94 |
In patients with viral etiology there was no difference in mortality between those who discontinued antibiotics compared to those who did not (1/8 [13%] vs. 3/26 [12%]; p = 1.00). LOS was shorter in inpatients who discontinued antibiotics (median days 5 [IQR 3β11.75] vs. 10.5 [IQR 6β19.25]; p = 0.05). Patients in whom antibiotics were continued despite a viral detection were as frequently admitted to ICU (11/26 [42%] vs. 5/8 [63%]; p = 0.55) or mechanically ventilated (6/26 [23%] vs. 1/8 [13%]; p = 0.93) as patients in whom antibiotics were discontinued. The proportion of patients with sepsis was comparable (16/26 [62%] vs. 6/8 [75%]; p = 0.80). These results were similar if adults and children were analyzed separately.
|
study
| 99.94 |
Normal CXR findings were significantly more frequent in patients with viral infection compared to bacterial infections (30% vs. 9%; p = 0.03). Multilobar infiltrates and pleural effusion on CXR were observed less often among subjects with viral infection (Tables 11, 12 and 13).Table 11Radiological findings for adult patients Viral Bacterial Mixed No pathogen p-value a (n = 40) (n = 36) (n = 6) (n = 100) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen X-ray, (n)3326581 Unilobar infiltrate, n (%)9 (27.3)5 (19.2)0 (0.0)14 (17.3)0.480.470.23 Multilobar infiltrates, n (%)6 (18.2)10 (38.5)2 (40.0)30 (37.0)0.090.560.05 Interstitial infiltrates, n (%)3 (9.1)7 (26.9)1 (20.0)17 (21.0)0.140.890.13 Pleural effusion, n (%)5 (15.2)11 (42.3)0 (0.0)24 (29.6)0.020.950.11 Normal, n (%)8 (24.2)2 (7.7)1 (20.0)14 (17.3)0.181.000.40Computer tomography, (n)2329571 Unilobar infiltrate, n (%)5 (21.7)4 (13.8)0 (0.0)7 (9.9)0.700.690.26 Multilobar infiltrates, n (%)11 (47.8)16 (55.2)4 (80.0)32 (45.1)0.600.420.82 Ground glass opacity, n (%)4 (17.4)6 (20.7)2 (40.0)29 (40.8)1.000.570.04 Pleural effusion, n (%)5 (21.7)13 (44.8)1 (20.0)25 (35.2)0.091.000.23 Normal, n (%)2 (8.7)0 (0.0)0 (0.0)0 (0.0)0.381.000.12 n number. Multiple findings were counted individually aMantel-Haenszel chi square test or Fisher exact test were used Table 12Radiological findings for pediatric patients Viral Bacterial Mixed No pathogen p-value a (n = 40) (n = 6) (n = 5) (n = 21) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen X-ray, (n)286516 Unilobar infiltrate, n (%)6 (21.4)0 (0.0)1 (20.0)2 (12.5)0.561.000.76 Multilobar infiltrates, n (%)6 (21.4)2 (33.3)4 (80.0)6 (37.5)0.880.040.42 Interstitial infiltrates, n (%)2 (7.1)1 (16.7)1 (20.0)2 (12.5)0.910.800.93 Pleural effusion, n (%)4 (14.3)2 (33.3)1 (20.0)2 (12.5)0.561.001.00 Normal, n (%)10 (35.7)1 (16.7)0 (0.0)3 (18.8)0.700.280.40Computer tomography, (n)5123 Unilobar infiltrate, n (%)2 (40.0)0 (0.0)0 (0.0)0 (0.0)1.000.950.71 Multilobar infiltrates, n (%)2 (40.0)1 (100.0)2 (100.0)3 (100.0)1.000.570.36 Ground glass opacity, n (%)0 (0.0)0 (0.0)1 (50.0)0 (0.0)n/a0.57n/a Pleural effusion, n (%)2 (40.0)1 (100.0)1 (50.0)2 (66.7)1.001.001.00 Normal, n (%)1 (20.0)0 (0.0)0 (0.0)0 (0.0)1.001.001.00 n number. Multiple findings were counted individually aMantel-Haenszel chi square test or Fisher exact test were used Table 13Radiological findings for all patients Viral Bacterial Mixed No pathogen p-value a (n = 80) (n = 42) (n = 11) (n = 121) Viral vs. bacterial Viral vs. mixed Viral vs. no pathogen X-ray, (n)61321097 Unilobar infiltrate, n (%)15 (24.6)5 (15.6)1 (10.0)16 (16.5)0.320.570.21 Multilobar infiltrates, n (%)12 (19.7)12 (37.5)6 (60.0)36 (37.1)0.060.030.02 Interstitial infiltrates, n (%)5 (8.2)8 (25.0)2 (20.0)19 (19.6)0.060.510.05 Pleural effusion, n (%)9 (14.8)13 (40.6)1 (10.0)26 (26.8)0.011.000.08 Normal, n (%)18 (29.5)3 (9.4)1 (10.0)17 (17.5)0.030.370.08Computer tomography, (n)2830774 Unilobar infiltrate, n (%)7 (25.0)4 (13.3)0 (0.0)7 (9.5)0.260.350.10 Multilobar infiltrates, n (%)13 (46.4)17 (56.7)6 (85.7)35 (47.3)0.440.140.94 Ground glass opacity, n (%)4 (14.3)6 (20.0)3 (42.9)29 (39.2)0.820.250.02 Pleural effusion, n (%)7 (25.0)14 (46.7)2 (28.6)27 (36.5)0.091.000.28 n number. Multiple findings were counted individually aMantel-Haenszel chi square test or Fisher exact test were used
|
study
| 99.94 |
In multivariate logistic regression (Tables 14 and 15), the absence of pleural effusion in adults was associated with detection of respiratory viruses (odds ratio [OR] 0.31, 95% confidence interval [CI] 0.12β0.80). For children, the lack of multilobar infiltrates was a significant predictor of respiratory virus detection (OR 0.22, 95% CI 0.06β0.81).Table 14Prediction of respiratory virus detection for adult patients Univariable analysis Multivariable analysis Predictor p-value OR (95% CI) p-value OR (95% CI) Neutropenia0.013.46 (1.32β9.07)0.272.11 (0.56β7.89) Hematologic malignancy0.042.25 (1.02β4.97)0.591.35 (0.45β4.01) Pleural effusion0.020.36 (0.15β0.86)0.020.31 (0.12β0.80) Platelets (minimum), G/l0.021.00 (0.99β1.00)0.201.00 (0.99β1.00) Table 15Prediction of respiratory virus detection for pediatric patients Univariable analysis Multivariable analysis Predictor p-value OR (95% CI) p-value OR (95% CI) Neutropenia0.067.75 (0.92β65.66)0.107.44 (0.69β80.42) Multilobular infiltrates0.030.31 (0.11β0.91)0.020.22 (0.06β0.81) White blood cells (maximum), G/l0.020.94 (0.89β0.99)0.100.95 (0.90β1.01) OR odds ratio, CI confidence interval
|
study
| 99.94 |
There are three main findings in this retrospective cohort study of the impact of viral multiplex rtPCR. First, the majority of patients with viral RTI received antibiotics and antibiotics were discontinued after viral detection in only a minority of patients. Second, when biomarkers, radiologic presentations and antibiotic pre-treatment were taken into account and categories of clinically bacterial and clinically viral infections were created (which more closely reflect clinical decision making), the multiplex rtPCR showed a greater impact and considerably improved correct management of clinically viral infections, from 67 to 100% among children and from 34 to 62% among adults. Third, the impact of rtPCR testing seemed to be more accentuated in children than in adults. More children than adults had an appropriate discontinuation of antibiotics, and the overall management of viral infections was superior in children compared to adults. Importantly, but with the caveat of small numbers, there was no evidence that outcome was worse in those with viral etiology who discontinued antibiotics compared to those who did not.
|
study
| 99.94 |
Several previous studies analyzed the impact of rapid availability of rtPCR results on antibiotic use. In a randomized controlled trial (RCT) of 107 adults with lower RTI, antibiotics were partially or totally discontinued in 6 (11%) of 55 patients for whom rtPCR results were available, albeit without overall reduction in antibiotic treatment duration . In a controlled clinical trial enrolling 583 children with acute RTI, Wishaupt et al. evaluated the diagnostic yield and effect of rapid communication of rtPCR results (within 12β36 h vs. 4 weeks after testing) and failed to show a significant influence on the duration of antibiotic treatment. In contrast, Brittain-Long et al. demonstrated in a RCT with 406 adults that patients randomized to rapid rtPCR results received antibiotics less frequently for acute RTI in a primary care setting during their initial visit (4.5% vs. 12.3%; p = 0.01). However, at the 10-day follow-up the prescription rates were similar again (13.9% vs. 17.2%; p = 0.36) . Contrary to these findings, a retrospective pre-post study of 1136 children showed that the introduction of an expanded multiplex rtPCR had a shorter turnaround time and decreased the duration of antibiotic use (2.8 vs. 3.2 days; p = 0.003) without reducing the proportion of antibiotic prescriptions .
|
study
| 74.4 |
As in most previous studies, typical respiratory bacteria were not included in the test panel. Due to this technical limitation, missing a treatable pathogen is of concern in light of potential bacterial-viral co-infections [3, 7β13, 16β19]. It was shown that clinical suspicion of a bacterial super-infection was one reason for physicians to not stop antibiotics in rtPCR-positive patients . We tried to partially overcome this by creating categories of clinically bacterial and clinically viral infections. This definition, aided by providing a biomarker criterion, accounted for the possibility of a viral infection in the setting of bacterial carriage. One of the major differences and advantages of the current study compared to previous publications is that it not only assessed the impact of the rtPCR results, which themselves had a limited impact on appropriate therapy, but it also integrated other βreal-worldβ clinical and radiologic parameters into the decision process.
|
study
| 100.0 |
Advanced molecular diagnostic tests have to be interpreted in the context of available clinical and diagnostic information in order to improve clinical management. The results confirmed the important role of clinical judgement for appropriate antibiotic prescriptions, with rtPCR providing additional information rather than being solely responsible for treatment decisions.
|
other
| 99.9 |
Quantification of genomic viral load might improve specificity of virus detection, with higher organism burden being associated with higher risk of complications and severe disease in adults and children [27, 28]. Unfortunately, quantitative results were not available with the applied assay. Similarly, optimal timing of molecular testing in relation to symptom onset and inclusion of an ever-expanding number of respiratory viruses might be important to further increase sensitivity . However, to the authorsβ knowledge, it has not yet been studied whether either of these two factors would improve clinical management.
|
review
| 99.44 |
A pathogen was identified in 140 (55%) patients in this study, in accordance with detection rates in other studies ranging from 38 to 82% [4, 12, 17, 19, 20, 22, 29β35]. A mixed bacterial-viral etiology was found in 11 (8%) patients. Previously described rates varied between 2 and 23% [17, 19, 22, 29β35]. Some studies suggested that mixed bacterial-viral infections result in more severe clinical diseases (as measured by the CURB-65 score or the pneumonia severity index) [17, 34], a higher rate of mechanical ventilation, longer duration of ICU care [36, 37], longer hospital stays [22, 36], or higher mortality [37, 38], while other studies did not [29, 39, 40]. In this study, mixed bacterial-viral infections were associated with a higher rate of ICU admission and mechanical ventilation compared to pure viral (p = 0.05; p = 0.005) and pure bacterial (p = 0.06; p = 0.19) infections if all patients were considered. However, these results should not be viewed as representative of the etiology of lower RTI in East Switzerland as these hospitals presented a preselected group of patients.
|
study
| 99.94 |
In agreement with the findings of some studies [20, 22, 34] and in contrast to others [7, 29, 39], this study failed to identify specific predictors of viral detection in multivariate logistic regression. Advancing age was previously described as more common in viral infections [19, 22, 29, 35] but the evidence is inconclusive [31, 32]. In this study, younger age was a significant predictor of virus detection in univariable logistic regression if all patients were considered, but not in stratified analyses in children and adults. The mean age in the group with respiratory viral infections was lower than in the remaining patients (29 vs. 47 years; p < 0.001) but the differences were not significant if stratified for children and adults.
|
study
| 99.94 |
There are some limitations to the study. First, the change of anti-infective management was retrospectively matched with the date of the rtPCR analysis. Exact time specifications were not available, leaving room for potential inaccuracies. It is not known whether and to what extent these or other factors contributed to the clinical decisions in starting, stopping, or continuing antibiotic therapy. Due to the retrospective nature of the study, it was not possible to consider the clinical presentation in the analysis. Therefore, it was difficult to reproduce the decision-making process and the primary indication for antibiotic therapy. This is an important limitation because clinical judgement remains essential concerning the use of antibiotics . Furthermore, data on the consequences of rtPCR results on antibiotic treatment are difficult to obtain in the ambulatory setting, which explains the relatively small number of enrolled outpatients. Prospective studies or ideally RCTs will be necessary to confirm the findings.
|
study
| 99.94 |
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