Microbiological evaluation of corneal and contact lens cultures in contact lens-associated bacterial keratitis

PurposeTo determine the degree of microbiological agreement between corneal scrapings and contact lens cultures in cases of contact lens-associated keratitis.MethodsElectronic medical records of all cases of contact lens-associated keratitis at a single institution from April 2006 to May 2019 were reviewed. Cases where both corneal scrapings and contact lens cultures were obtained were included in the study. Group 1 demonstrated agreement between corneal scrapings and contact lens cultures. Group 2 demonstrated growth on both cultures, but disagreement in isolated organism. Group 3 demonstrated negative corneal cultures but growth on contact lens cultures and the diagnostic yield of contact lens microbiological cultures and agreement between corneal and contact lens cultures.ResultsA total of 80 eyes of 72 patients were included in the study. 135 total incidences of microbiological results were included for data analysis. Group 1 contained nine incidences (6.7%), group 2 contained 60 incidences (44.4%) and group 3 contained 66 incidences (49%). In group 3, 50% of the cases were treated based on contact lens culture data. There was no statistically significant difference between all three groups in terms of baseline characteristics, presenting vision, vision at last follow-up, number of antibiotics used or complications from keratitis. Pseudomonas was the most common microorganism isolated, and in 89% of these cases, there was disagreement between corneal and contact lens cultures.ConclusionsAlthough there was a disagreement in the microbiological yield between contact lens and corneal cultures, contact lens cultures were useful in management of patients while achieving similar outcomes.

How do we construct and operate experimental streams? An overview of facilities, protocols, and studied questions

Experimental streams are bounded and partly enclosed lotic units that facilitate the simulation of certain aspects of natural stream ecosystems under controlled conditions. We summarized the current knowledge regarding experimental streams in order to support researchers in designing and undertaking future studies using experimental streams. We observed an increase in the number of such studies since 1975. The geographically uneven distribution of studies suggests that the generalization of findings to global scale may not be straightforward. Our results indicate that macroinvertebrates, fish, and algae are the most frequently studied organisms and that the size of the experimental streams was related to the focal organism group(s) studied. The size of the units decreased over time, while the number of treatments, interpreted as the combination of the levels of factors, increased. These results suggest that biologically complex studies have gradually been replaced by biologically less complex ones. In contrast, the experimental complexity (the number of treatments) and the statistical power (number of replication) increased. Finally, we identified a number of important, but poorly documented pieces of information regarding experimental stream systems and experimental protocols and made recommendations for future research.

Antimycobacterial Susceptibility Testing of Nontuberculous Mycobacteria

ABSTRACT Recommendations for first-line and second-line drug testing and organism group, specific methodologies, and reporting recommendations have been addressed by the Clinical and Laboratory Standards Institute (CLSI) and are important in the selection of appropriate antimicrobial treatment regimens for nontuberculous mycobacteria (NTM) disease. This review also includes recent information on new antimicrobials proposed for the treatment of NTM but not yet addressed by the CLSI and molecular (gene sequencing) methods associated with the detection of antimicrobial resistance of two major therapeutic antimicrobials, clarithromycin and amikacin.

mirtronDB: a mirtron knowledge base

Motivation Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB currently contains a total of 1407 mirtron precursors and 2426 mirtron mature sequences in 18 species. Results Through a user-friendly interface, users can now browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource that provides free and user-friendly access to knowledge on mirtron data. Availability and implementation MirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/. Supplementary information Supplementary data are available at Bioinformatics online.

Contrasting Responses among Aquatic Organism Groups to Changes in Geomorphic Complexity Along a Gradient of Stream Habitat Restoration: Implications for Restoration Planning and Assessment

Many stream restoration projects aim to increase geomorphic complexity, assuming that this increases habitat heterogeneity and, thus, biodiversity. However, empirical data supporting these linkages remain scant. Previous assessments of stream restoration suffer from incomplete quantification of habitat complexity, or a narrow focus on only one organism group and/or one restoration measure, limiting learning. Based on a comprehensive quantification of geomorphic complexity in 20 stream reaches in northern Sweden, ranging from streams channelized for timber floating to restored and reference reaches, we investigated responses of macroinvertebrates, diatoms, and macrophytes to multiple geomorphic metrics. Sediment size heterogeneity, which was generally improved in restored sites, favored macroinvertebrate and diatom diversity and macroinvertebrate abundance. In contrast, macrophyte diversity responded to increased variation along the longitudinal stream profile (e.g., step-pools), which was not consistently improved by the restoration. Our analyses highlight the value of learning across multiple restoration projects, both in identifying which aspects of restoration have succeeded, and pinpointing other measures that might be targeted during adaptive management or future restoration. Given our results, a combination of restoration measures targeting not only sediment size heterogeneity, but also features such as step-pools and instream wood, is most likely to benefit benthic biota in streams.

mirtronDB: a mirtron knowledge base

MotivationMirtrons are originated from short introns with atypical cleavage from the miRNA canonical pathway by using the splicing mechanism. Several studies describe mirtrons in chordates, invertebrates and plants but in the current literature there is no repository that centralizes and organizes these public and available data. To fill this gap, we created the first knowledge database dedicated to mirtron, called mirtronDB, available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB has a total of 1,407 mirtron precursors and 2,426 mirtron mature sequences in 18 species.ResultsThrough a user-friendly interface, users can browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource to explore mirtrons and their regulations, providing free, user-friendly access to knowledge on mirtron data.AvailabilityMirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/[email protected] informationSupplementary data are available.

Multicenter Clinical Evaluation of BacT/Alert Virtuo Blood Culture System

ABSTRACTBacT/Alert Virtuo is an advanced, automated blood culture system incorporating improved automation and an enhanced detection algorithm to shorten time to detection. A multicenter study of the investigational Virtuo system (bioMérieux, Inc., Durham, NC) compared to BacT/Alert 3D (BTA3D) for detection of bacteremia/fungemia in four bottle types, SA and FA Plus (aerobic) and SN and FN Plus (anaerobic), was performed in a clinical setting with patient samples in a matched system design clinical trial. Blood was added to paired aerobic or anaerobic bottles, with the volume in each bottle in each pair required to be ≤10 ml and with the volumes required to be within 30% of each other. Of 5,709 bottle sets (52.5% aerobic pairs and 47.5% anaerobic pairs), 430 (7.5%) were positive for bacterial or fungal growth, with 342 (6.0%) clinically significant and 83 (1.5%) contaminated. A total of 3,539 sets (62.0%) were volume compliant, with 203 sets (5.7%) clinically significant. The positivity rates for volume-compliant bottle pairs determined by the two systems were comparable, with 68.7% of clinically significant isolates detected by both instruments, 15.7% by Virtuo only, and 15.7% by BTA3D only. Virtuo detected microbial growth nearly 2 h sooner overall than BTA3D (mean, 15.9 h versus 17.7 h). Shorter time to detection by Virtuo was related to organism group, with the time to detection being significantly shorter for enteric Gram-negative bacilli and enterococci (means, 3.6 h and 2.3 h shorter, respectively). This large clinical study demonstrated that the Virtuo blood culture system produced results comparable to those seen with the long-established BTA3D system, with significantly shorter time to detection.

Comparative Killing Rates of Fluoroquinolones and Cell Wall-Active Agents

ABSTRACT Killing rates of fluoroquinolones, β-lactams, and vancomycin were compared against Enterobacteriaceae, Staphylococcus aureus, pneumococci, streptococci, and Enterococcus faecalis. The times required for fluoroquinolones to decrease viability by 3 log10 were 1.5 h forEnterobacteriaceae, 4 to 6 h for staphylococci, and ≥6 h for streptococci and enterococci. Thus, the rate of killing by fluoroquinolones is organism group dependent; overall, they killed more rapidly than β-lactams and vancomycin.

Controlled Comparative Evaluation of BacT/Alert FAN and ESP 80A Aerobic Media as Means for Detecting Bacteremia and Fungemia

During a one-year period, a total of 6,305 blood cultures were processed in a tertiary-care teaching hospital; 6 to 12 ml of blood was inoculated into both a BacT/Alert Fan aerobic bottle and an ESP 80A aerobic bottle. The FAN aerobic bottle contains an antimicrobial-absorbing material; the 80A aerobic bottle does not. Bottles were processed on their respective continuous-monitoring blood culture instruments for up to five days of incubation. Four hundred thirty-three cultures (6.9%) representing 301 septic episodes in 235 different patients yielded 490 bacteria or yeasts thought to be clinically significant. Two hundred seventy-five of the 433 presumed clinically significant positive cultures (63.5%) representing 195 septic episodes and yielding 301 isolates were positive in both FAN and 80A bottles. One hundred nine significant positive cultures (25.2%) (i.e., cultures positive with an organism judged to be of probable clinical significance) from 70 septic episodes yielded 126 isolates only in FAN bottles. Conversely, the 80A bottle was exclusively positive in 49 instances (11.3%), representing 36 septic episodes and yielding 63 isolates. The higher rates of significant positive blood cultures, numbers of septic episodes documented, and numbers of isolates recovered in FAN bottles versus 80A bottles were all statistically significant (P < 0.05). Enhanced rates of detection of presumed clinically significant isolates in FAN bottles were largely accounted for by Staphylococcus aureus, members of the Enterobacteriaceae, and non-Pseudomonas aeruginosa miscellaneous gram-negative bacilli from patients receiving antimicrobial therapy at the time blood cultures were obtained. Enhanced recovery of one organism group, the β-hemolytic streptococci, occurred in 80A. With one exception, detection times were essentially equivalent in the two systems. The single exception pertained to streptococci and enterococci, which were recovered significantly faster in 80A bottles. Three hundred thirty-eight of the 6,305 blood cultures evaluated in this study (5.4%) were judged likely to be contaminated. The percentages of probable contaminated cultures were as follows: 26.6% FAN and 80A; 42.3% FAN only; 31.1% 80A only (P < 0.05). Finally, the instrument false-positive rates for the two systems were 0.7% with FAN and 3.0% with 80A (P < 0.05). We conclude that while contamination rates were slightly higher with FAN than with 80A, use of FAN aerobic bottles in conjunction with the BacT/Alert system will yield significantly higher numbers of clinically significant blood culture isolates than 80A bottles and the ESP system. Furthermore, this enhanced detection is most conspicuous in patients receiving antimicrobial therapy at the time blood cultures are performed, probably due to the presence of an antimicrobial-absorbing material in FAN aerobic bottles.

Effects of a mixture of organisms,Lactobacillus acidophilusorStreptococcus faecalison cholesterol metabolism in rats fed on a fat- and cholesterol-enriched diet

The effect of a mixture of organisms (a probiotic mixture) comprisingBacillus, Lactobacillus, Streptococcus, Clostridium, SaccharomycesandCandida(107–8colony-forming units/g rice bran of each component) on lipid metabolism was compared with that ofL. acidophilusand that ofS. faecalis. There were four treatment groups: rice bran (control), the mixture of organisms,L. acihphifusorS. faecds(30g/kg) were given to rats in a fat- and cholesterol-enriched diet for 4 weeks. The serum total cholesterol concentration of the group fed on the mixture of organisms was reduced by 15–33% compared with the other groups at the end of the 4week feeding period (P< 0·05). This group also had a lower hepatic cholesterol concentration (36–44%) than the two single-bacteria groups (P< 0·05). 3-Hydmxy-3-methylglutaryl-Co A reductase (NADPH; EC 1.1.1.34) activities of the mixed-organism andL. acidophifusgroups were significantly lower (61–63%) than those of the other groups (P< 0·05); the activity of the S. faecalis group was also signikantly lower (42%) than that of the control group (P< 0·05). The faecal cholesterol and bile acid concentrations of the mixed-organism group increased compared with those of theL. acidophilusandS. faecalisgroups (P< 0·05). The capacity of the mixed- organism cells to bind bile saltin vitrowas significantly higher (approximately 50%) than that of the singlebacteria cells (P< 0·05). On the other hand, cholesterol micelle formation for the mixed-organism cells was significantly (approximately 9%) lower than that of the singlebacteria cells (P< 0·05). These results indicate that the mixture of organisms decreased the synthesis of cholesterol in the liver and increased the loss of steroids from the intestine, in rats. Thus, the mixture of organisms had a hypocholeaterolaemic role