Effects of azithromycin and doxycycline on the vaginal microbiota of women with urogenital Chlamydia trachomatis infection: a substudy of the Chlazidoxy randomized controlled trial.

OBJECTIVES: Dysbiotic bacterial communities within the vagina are associated with Chlamydia trachomatis infection. We compared the effect of treatment with azithromycin and doxycycline on the vaginal microbiota in a cohort of women with a urogenital C. trachomatis infection randomly assigned to one of these treatments (Chlazidoxy trial). METHODS: We analysed vaginal samples from 284 women (135 in the azithromycin group and 149 in the doxycycline group) collected at baseline and 6 weeks after treatment initiation. The vaginal microbiota was characterized using 16S rRNA gene sequencing and classified into community state types (CSTs). RESULTS: At baseline, 75% (212/284) of the women had a high-risk microbiota (CST-III or CST-IV). A cross-sectional comparison 6 weeks after treatment showed that 15 phylotypes were differentially abundant, but this difference was not reflected at the CST (p 0.772) or diversity level (p 0.339). Between baseline and the 6-week visit, α-diversity (p 0.140) and transition probabilities between CSTs were not significantly different between the groups, and no phylotype was differentially abundant. DISCUSSION: In women with urogenital C. trachomatis infection, the vaginal microbiota does not seem to be affected by azithromycin or doxycycline 6 weeks after treatment. Because the vaginal microbiota remains susceptible to C. trachomatis infection (with CST-III or CST-IV) after antibiotic treatment, women remain at risk of reinfection, which could originate from unprotected sexual intercourse or untreated anorectal C. trachomatis infection. This last consideration advocates for the use of doxycycline instead of azithromycin because of its higher anorectal microbiological cure rate.

SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species.

Background: For several decades, an increase in disease or pest emergences due to anthropogenic introduction or environmental changes has been recorded. This increase leads to serious threats to the genetic and species diversity of numerous ecosystems. Many of these events involve species with poor or no genomic resources (called here "orphan species"). This lack of resources is a serious limitation to our understanding of the origin of emergent populations, their ability to adapt to new environments and to predict future consequences to biodiversity. Analyses of genetic diversity are an efficient method to obtain this information rapidly, but require available polymorphic genetic markers. New information: We developed a generic bioinformatics pipeline to rapidly isolate such markers with the goal for the pipeline to be applied in studies of invasive taxa from different taxonomic groups, with a special focus on forest fungal pathogens and insect pests. This pipeline is based on: 1) an automated de novo genome assembly obtained from shotgun whole genome sequencing using paired-end Illumina technology; 2) the isolation of single-copy genes conserved in species related to the studied emergent organisms; 3) primer development for multiplexed short sequences obtained from these conserved genes. Previous studies have shown that intronic regions of these conserved genes generally contain several single nucleotide polymorphisms within species. The pipeline's functionality was evaluated with sequenced genomes of five invasive or expanding pathogen and pest species in Europe (Armillariaostoyae (Romagn.) Herink 1973, Bursaphelenchusxylophilus Steiner & Buhrer 1934, Sphaeropsissapinea (fr.) Dicko & B. Sutton 1980, Erysiphealphitoides (Griffon & Maubl.) U. Braun & S. Takam. 2000, Thaumetopoeapityocampa Denis & Schiffermüller, 1775). We successfully isolated several pools of one hundred short gene regions for each assembled genome, which can be amplified in multiplex. The bioinformatics pipeline is user-friendly and requires little computational resources. This easy-to-set-up and run method for genetic marker identification will be useful for numerous laboratories studying biological invasions, but with limited resources and expertise in bioinformatics.

Laser Flare Photometry: A Useful Tool for Monitoring Patients with Juvenile Idiopathic Arthritis-associated Uveitis.

PURPOSE: We evaluated laser flare photometry (LFP) values in patients with juvenile idiopathic arthritis (JIA)-associated uveitis. METHODS: Retrospective study. A decrease of the LFP value between baseline visit and 1 month after anti-inflammatory treatment intensification allowed us to define two groups of patients: group 1 (decreased LFP value ≥50%) and group 2 (<50%). We evaluated the prevalence of vision-threatening complications in both groups. RESULTS: Fifty-four patients (87 eyes) were followed for 9.9 ± 5 years. Group 1 eyes (n = 54) had significantly fewer ocular complications than group 2 eyes (n = 33) at both 5 years visit (p = .03) and final visit (p = .047). At the final visit, group 2 eyes had significantly more band keratopathy, trabeculectomy, cataract surgery, glaucoma and papille edema. Group 1 eyes kept a better visual acuity (p < .0001). CONCLUSION: The decrease of LFP values ≥50% of the initial value 1 month after treatment intensification is a good early prognostic factor.

Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes.

Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (i.e., unbalanced representation of source populations); and iii) the reproduction mode (e.g., selfing, vegetative propagation). If a source population was not represented in the data set, no bias was observed in inference accuracy for regions originating from represented sources and regions from the missing source were assigned differently depending on the methods. Overall, the selected ancestry inference methods may be used for crop plant analysis if all ancestral sources are known.

Metatranscriptomic exploration of microbial functioning in clouds.

Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.

Risk assessment of sudden visual loss following non-penetrating deep sclerectomy in severe and end-stage glaucoma.

BACKGROUND/OBJECTIVES: To assess the risk of immediate sudden visual loss ("wipe-out" phenomenon) following non-penetrating deep sclerectomy (NPDS) for end-stages glaucoma within the first 6-months postoperative period. SUBJECTS/METHODS: Monocenter database study. We reviewed the results for 73 eyes with severe or end-stage glaucoma that underwent NPDS. End-stage glaucoma (stage 5) was defined by the inability of patients to perform the Humphrey visual field test or by a visual acuity <20/200 due to glaucoma, according to the Glaucoma Staging System classification. Severe glaucoma (stage 4) was defined by a mean deviation (MD) <-20 dB by the preoperative 24-2 Humphrey visual field assessment. All eyes had a severe defect on the central 10° visual field: only a central island of vision remained. "Wipe-out" was defined as the permanent postoperative reduction of visual acuity to <20/200 or to "counting fingers" or less if preoperative visual acuity was <20/200. RESULTS: The mean age was 60 years (range 22-86). Before surgery, the average MD (Humphrey 24-2) was -25.6 ± 3.8 dB, the MD (Humphrey 10-2) -19.9 ± 7.0 dB, and the VFI 24.6 ± 13%. There were no cases of postoperative flat anterior chamber. No patients experienced "wipe-out" within the first 6 months following surgery. At the six-month visit, intraocular pressure (IOP) had decreased significantly from 22.0 ± 8.8 to 13.5 ± 4.5 mmHg (P<0.001). There were no significant changes in mean visual acuity after 6 months (P = 6). CONCLUSIONS: In our study, NPDS provided considerable IOP decrease with no occurrences of "wipe-out" and few other complications. Consideration of NPDS in end-stage and severe glaucoma is advisable given its low risk of intraoperative and postoperative complications and the low risk of wipe out. This surgery should probably be offered with less apprehension about the risk of "wipe-out" in end-stages glaucoma.

Outcomes of Laser Goniopuncture Following Nonpenetrating Deep Sclerectomy With Mitomycin C: A Large Retrospective Cohort Study.

PURPOSE: To report on the frequency, efficacy, and safety of laser goniopuncture (LGP) in lowering intraocular pressure (IOP) following mitomycin-C-augmented nonpenetrating deep sclerectomy (NPDS) in a large cohort of eyes. MATERIALS AND METHODS: This is a monocenter database retrospective study. We reviewed records of 350 eyes that underwent NPDS between 2009 and 2015, at the National Ophthalmology Center of XV-XX (Paris, France). We recorded the incidence of LGP, the time between NPDS and LGP, IOP efficacy, and the occurrence of complications. The success of the LGP was defined by an IOP<15 mm Hg without hypotonic treatment. RESULTS: The mean postoperative follow-up period was 19±15.9 months after the NPDS (range, 6 to 58). LGP was performed in 125 eyes (35.7%) in a mean time after NPDS of 7.4±7.6 months (range, 1 d to 36 mo). Most LGP procedures were performed during the first year (97 eyes, 77.6%). The survival analysis using the Kaplan-Meier method showed a 50% incidence of LGP by 2 years. The mean IOP before LGP was 23.8±7.1 mm Hg. LGP resulted in immediate (day 8) and significant IOP lowering by up to 15±6.8 mm Hg. This decrease was maintained throughout the follow-up period, and the Kaplan-Meier survival success rate at 2 years was 48.9% (95% confidence interval, 39.4-60.8). The most common complication was iris incarceration, which occurred in 22 eyes of 125 LGP (17.6%). CONCLUSIONS: Most of the eyes that underwent NPDS may require LGP to reduce the IOP to below the target value. Most often, this procedure was performed in the first year after NPDS (77.6%). LGP lowered IOP<15 mm Hg without any hypotonic medication for at least 2 years in 50% of cases. Goniopuncture is associated with potentially significant complications, of which the most common is iris incarceration. We identified 2 predicting factors for iris incarceration: high IOP before LGP and early LGP after NPDS.

Correction to: Central 10-degree visual field change following non-penetrating deep sclerectomy in severe and end-stage glaucoma: preliminary results.

The published online version contain mistake in the author list. The correct presentation is also given above.

Central 10-degree visual field change following non-penetrating deep sclerectomy in severe and end-stage glaucoma: preliminary results.

PURPOSE: To report the impact of non-penetrating deep sclerectomy (NPDS) in severe and end-stage glaucoma treatment on the central 10° visual field progression (mean deviation, four central points, foveal threshold) and assess the risk of sudden visual loss. METHODS: Monocenter database study. We reviewed records of 34 eyes with severe or end-stage glaucoma that underwent NPDS between 2009 and 2015, at the National Ophthalmology Center of XV-XX (Paris, France). Severe and end-stage glaucoma were defined according to the Bascom Palmer Modified Glaucoma Staging System classification. All eyes had a constricted visual field < 10° (severe injury by the Humphrey visual field automated (HVFA) 10-2). Visual fields were recorded every 6 months after the procedure. Data from the last visit was used for the statistical analysis. RESULTS: The mean follow-up duration was 29 months (range 6 to 54) and 33 (97%) eyes were followed for more than 1 year. There were no cases of postoperative sudden visual loss. The intraocular pressure (IOP) decreased from 21.9 ± 8.1 to 15.0 ± 5.4 mmHg (P < .001). Twenty-eight (82%) eyes had an IOP < 21 mmHg and 19 (56%) an IOP < 16 mmHg. The MD 10-2 remained stable (- 19.8 ± 7.4 to - 19.4 ± 8.1 dB, non-significant improvement of + 0.4 dB, P = .1). The MD 10-2 slope showed an insignificant improvement of + 0.25 ± 1.8 dB per year (dB/y) (P = 0.1), but this slope was significantly better when the IOP was reduced to < 16 mmHg than when the IOP was ≥ 16 mmHg at the last visit (+ 0.84  1.2 versus - 0.48 ± 2.2 dB/y, P = .05). The mean number of the four central test points with sensitivity ≤ 5 dB and the change in mean sensitivity of the four central field points remained stable. There were no significant changes in the VFI (from 25.4% ± 13 to 25.8% ± 20) and in foveal threshold. CONCLUSION: NPDS appears to provide stability of the central 10° visual field (with a trend towards improvement but non-significant) with no occurrence of "wipe-out" phenomenon and few other complications. Consideration of NPDS in end-stage and severe glaucoma is advisable given its low risk of complications and its considerable IOP decrease with a relative stability of the central visual field.